Modified phycobilisomes and uses therefore

ABSTRACT

This invention provides modified phycobilisomes and phycobilisome complexes that are supramolecular complexes with diverse spectral properties, and which may optionally be immobilized on a manufactured solid support. The invention provides a versatile set of highly sensitive signal-generating systems and conjugates that may be used as highly detectable tracers and labels, or in biotransducers comprising phycobilisomes or phycobilisome complexes, and also provides methods for performing specific binding assays using signal-generating systems comprising phycobilisomes as detectable labels. The embodiments of the invention provide the art with an extremely sensitive, nonisotopic detection means for assaying analytes and for sensing molecular events and environmental conditions.

[0001] This application is a continuation-in-part of application Ser.No. 08/600,359, filed Feb. 13, 1996, which is in turn acontinuation-in-part of application Ser. No. 08/420,726, filed Apr. 10,1995, and now issued as U.S. Patent No. ______. The prior applicationsare incorporated herein by reference in their entirety.

BACKGROUND OF THE INVENTION

[0002] Phycobilisomes are complexes of phycobiliproteins and colorlesspolypeptides which function as the major light harvesting antennae inblue-green and red algae (Gantt, (1975) “Phycobilisomes: lightharvesting pigment complexes,” BioScience 25:781-788).Naturally-occurring phycobilisomes from different organisms share anumber of common properties, including: (1) extremely high “complexmolecular weights” (5-20×10⁶ daltons) i.e., the weight of one mole of aphycobilisome complex comprised of multiple molecules; (2) multipleabsorption maxima in the visible range of the electromagnetic spectrum;(3) high molar absorptivities (e_(max)>10⁷ M⁻¹ cm⁻¹); (4) efficient(>90%) directional vibrational energy transfer among constituentphycobiliproteins, commonly from one or more sensitizing species to aterminal acceptor capable of fluorescence; (5) large Stokes shiftsrelative to isolated phycobiliproteins; (6) high quantum yields ofconstituent phycobiliproteins; (7) high solubility in aqueous buffers;(8) allophycocyanin-containing core structures; and (9) preciselydefined phycobiliprotein and linker polypeptide composition andsupramolecular organization.

[0003] Morphologically, phycobilisomes are complex assemblies ofoligomeric phycobiliprotein discs arranged in ordered stacks referred toas “rods”. In general, several arm-like rods radiate out from a coreassembly, also comprised of rods. Phycobilisomes from differentorganisms are morphologically and stoichiometrically diverse, havingdifferent numbers and types of constituent phycobiliproteins and rods.In general, peripheral rods are comprised of phycoerythrocyanin,phycoerythrin, and/or phycocyanin and associated linker proteins, andthe core is comprised of allophycocyanin and associated linker proteins.The colorless polypeptides are involved in the assembly and positioningof the phycobiliproteins within the phycobilisomes for proper stabilityand energy transfer. The major criterion for the functional integrity ofthese complexes is the demonstration that they exhibit highly efficienttransfer of energy between component phycobiliproteins, for example, inPorphyridium cruentum phycobilisomes from phycoerythrin (PE) tophycocyanin (PC) and finally to allophycocyanin (APC).

[0004] Supramolecular complexes comprising phycobilisomes are well-knownin the art, as evidenced by the substantial body of literature onpreparative methods (e.g., Gantt, E. 1986, “Phycobilisomes. In:Photosynthesis III: Photosynthetic Membranes and Light HarvestingSystems” (L. A. Staehelin and C. J, Arntzen, eds.), pp. 260-268,Springer-Verlag, NY; Grossman, A. R. et al. 1993, “The phycobilisome, alight-harvesting complex responsive to environmental conditions,”Microbiological Reviews 57:725-749; Hiller, et al., 1982, “Isolation ofintact detergent-free phycobilisomes by trypsin.” FEBS Lett.156:180-184), rod and core subassemblies (e.g., Lundell, et al. 1983a,“Molecular architecture of a light-harvesting antenna: core substructurein Synechococcus 6301 phycobilisomes: two new allophycocyanin andallophycocyanin B complexes,” J. Biol. Chem., 258:902-908; Lundell, etal., 1983b, “Molecular architecture of a light-harvesting antenna:quaternary interactions in the Synechococcus 6301 phycobilisome core asrevealed by partial tryptic digestion and circular dichroism studies,”J. Biol. Chem., 258:8708-8713; Lundell, et al., 1983c, “Moleculararchitecture of a light-harvesting antenna: structure of the 18Score-rod subassembly of the Synechococcus 6301 phycobilisome,” J. Biol.Chem., 258:894-901; Glazer, A. N. 1985a, “Light harvesting byphycobilisomes,” Annual Rev. Biophys. and Biophys. Chem., 14:47-77),phycobilisome-photosystem complexes (e.g., Diner, B.A. 1979, “Energytransfer from phycobilisomes to photosystem II reaction centers in wildtype Cyanidium caldarium,” Plant Physiol., 63:30-34; Gantt E, et al.(1988), “Photosystem II-phycobilisome complex preparations,” Meth.Enzymol. 167, 286-290; Clement-Metral, J. D. and Gantt (1983a),“Isolation of oxygen-evolving phycobilisome-photosystem II particlesfrom Porphyridium cruentum,” FEBS Letters 156:185-188; Clement-Metral JD, et al. (1983b), “A photosystem II-phycobilisome preparation from thered alga Porphyridium cruentum: oxygen evolution, ultrastructure, andpolypeptide resolution,” Arch. Biochem. Biophys. 238:10-17; KirilovskyD, et al. (1986). “Functional assembly in vitro of phycobilisomes withisolated photosystem II particles of eukaryotic chloroplasts,” J. Biol.Chem., 261:12317-12323), phycobilisome-membrane preparations (e.g.,Clement-Metral, J. D., et al. (1971), “Fluorescence transfer inglutaraldehyde fixed particles of the red alga Porphyridium cruentrum(N),” FEBS Letters 12:225-228), phycobilisome dissociation (e.g., Rigbi,et al. (1980), “Cyanobacterial phycobilisomes: Selective dissociationmonitored by fluorescence and circular dichroism.” Proc. Natl. Acad.Sci. USA, 77:1961-1965) and reconstitution (e.g., Gantt, et al. (1979),“Phycobilisomes from blue-green and red algae: Isolation criteria anddissociation characteristics,” Plant Physiology 63:615-620; Kirilovskyet al. (1986), Glick, et al. (1983), “Role of the colorless polypeptidesin phycobilisome reconstitution from separated pycobiliproteins,” PlantPhysiol., 69:991-997), genetic modifications (e.g., Bryant, D. A., 1991,“Cyanobacterial phycobilisomes: progress toward complete structural andfunctional analysis via molecular genetics,” In L. Bogorad and I. K.Vasil (ed.), Cell Culture and Somatic Genetics of Plants. MolecularBiology of Plastids and Mitochondria, Vol. 7, pp. 257-300, AcademicPress, San Diego, Calif.); Yamanaka, et al. (1978), “Cyanobacterialphycobilisomes. Characterization of the phycobilisomes of Synechococcussp. 6302,” J. Biol. Chem., 253:8303-8310; Yamanaka, et al. (1980),“Molecular architecture of a light-harvesting antenna. Comparison ofwild type and mutant Synechococcus 6301 phycobilisomes,” J. Biol. Chem.,255:11004-11010), and environmental effects (e.g., Grossman et al.(1993)), including chromatic adaptation (e.g., Bryant, et al. 1981,“Effects of chromatic illumination on cyanobacterial phycobilisomes:Evidence for the specific induction of a second pair of phycocyaninsubunits in Pseudanabaena 7409 grown in red light,” Eur. J. Biochem.119:415-424).

[0005] Isolated phycobilisomes readily dissociate into freephycobiliproteins and a variety of phycobiliprotein complexes under allbut the most favorable conditions. Low to moderate ionic strength (<0.5M phosphate), low phycobilisome concentration (<1 mg/ml), and low andhigh temperatures lead to dissociation of phycobilisomes (Katoh, (1988)Methods in Enzymology, 162:313-318; Gantt et al., (1979)). Freezing ofalgae is also reported to lead to destruction of phycobilisomes (Ganttet al., (1972) Journal of Cell Biology, 54:313-324).

[0006] Isolated phycobiliproteins, the component fluorescent proteins ofphycobilisomes, have been used as labels in immunoassays. See e.g.,Stryer et al., U.S. Pat. No. 4,520,110 and Kronick et al. (1983)Clinical Chemistry, 29:1582-1586. However, because of the difficulty inisolating and manipulating intact phycobilisomes, the art has notrecognized that these macromolecular assemblies could be similarlyutilized. Because the signal which phycobilisomes can provide istheoretically so much larger than that of isolated phycobiliproteins,there is a need in the art for methods of treating phycobilisomes sothat they can be used as detectable markers for a host of assays andother applications.

SUMMARY OF THE INVENTION

[0007] One object of this invention is to provide supramolecularcomplexes with diverse spectral properties for use as highly detectabletracers and labels.

[0008] Another object of this invention is to provide a versatile set ofhighly sensitive signal-generating systems and conjugates for use in,inter alia, various assay methods.

[0009] Yet another object of this invention is to provide biotransducerscomprising phycobilisomes or phycobilisome complexes immobilized on amanufactured solid support.

[0010] Still another object of this invention is to provide methods forperforming specific binding assays using signal-generating systemscomprising phycobilisomes as detectable labels. These and otherintentions of this invention are achieved by one or more of thefollowing embodiments.

[0011] In one embodiment, this invention provides an isolated, soluble,stabilized phycobilisome comprising two or more phycobiliproteinsspecifically connected by at least one linker polypeptide. Thestabilized phycobilisome of this embodiment may comprise at least oneperipheral rod, or a core complex and no peripheral rods, or a corecomplex, and at least one disc. In one mode, the stabilizedphycobilisome of this embodiment comprises an anchor polypeptide. In aparticular mode, the different proteins making up the stabilizedphycobilisome of this embodiment are not all found in a single algalstrain, but rather are proteins whose sequences are encoded by more thanone distinct algal strain; in other words, some of the proteins makingup the phycobilisomes of this mode may originally derive from an algalstrain different from the strain that is the source of other proteins inthe phycobilisome. In another particular mode, the stabilizedphycobilisome is reconstituted from a mixture containing phycobilisomecomponents, which may include isolated phycobiliproteins and/or isolatedlinker polypeptides, and optionally partially reconstitutedphycobilisomes. In a preferred mode of this embodiment, the stabilizedphycobilisome is modified by covalent attachment of desired chemicalmoieties, the chemical moieties optionally being attached to aparticular portion of the phycobilisome. In yet another mode, theisolated, stabilized phycobilisome of this embodiment is functionallycoupled to another signal-generating system.

[0012] In another embodiment, this invention provides a phycobilisomeconjugate comprising a phycobilisome conjugated to a molecular speciesselected from the group consisting of ligands, receptors, andsignal-generating molecules, where the phycobilisome comprises aplurality of phycobiliproteins specifically connected by at least onelinker polypeptide, the molecular species preferably being attached to asingle type of phycobiliprotein or a single type of linker polypeptideor an anchor peptide. Alternatively, the molecular species may beattached to a particular portion of the phycobilisome. In one mode ofthis embodiment, the phycobilisome comprises at least one proteinencoded by each of at least two different algal strains. In analternative mode of this embodiment, the phycobilisome is reconstitutedfrom a mixture containing isolated phycobiliproteins, isolated linkerproteins, or a mixture thereof. In yet another mode of this embodiment,the phycobilisome is functionally coupled to a signal-generating system.The molecular species conjugated to the phycobilisome may be, forexample, streptavidin, avidin, an antibody, biotin, a drug, an antigen,a hapten, a nucleic acid, a carbohydrate, or a lectin.

[0013] In yet another embodiment, this invention provides an isolated,functionally intact phycobilisome comprising a plurality ofphycobiliproteins specifically connected by at least one linkerpolypeptide, where the phycobilisome is immobilized on a solid support.In a preferred mode of this embodiment, the immobilized phycobilisome isstabilized. In another preferred mode, the immobilized phycobilisome iscovalently attached to a molecular species selected from the groupconsisting of ligands, receptors, and signal-generating molecules, andmore preferably, the molecular species is attached to one type ofconstituent phycobilisome protein or to a particular portion of thephycobilisome. In one mode of this embodiment, the immobilizedphycobilisome comprises at least one protein encoded by each of at leasttwo different algal strains. In an alternative mode of this embodiment,the immobilized phycobilisome is reconstituted from a mixture containingisolated phycobiliproteins, isolated linker proteins, or a mixturethereof. In yet another mode of this embodiment, the immobilizedphycobilisome is functionally coupled to another signal-generatingsystem. Alternatively, the immobilized phycobilisome may be a functionalcomponent of a biotransducer. The solid support may be selected from thegroup consisting of a synthetic membrane, a polymer, a microparticle,silicon, and glass. In a particular mode of this embodiment, theinvention provides a manufactured solid support containing a pluralityof immobilized phycobilisomes, where the phycobilisomes are immobilizedon the solid support in a structurally ordered arrangement therebyforming a pattern on the solid support. In an alternative mode of thisembodiment, the invention provides a manufactured solid supportcontaining a plurality of immobilized phycobilisomes, where thephycobilisomes are all immobilized on the solid support in the sameorientation with respect to the solid support.

[0014] In still another embodiment, this invention provides an inputsystem for a transducer comprising conversion means for receivingultraviolet or visible light and directionally transferring light energyof this light; and coupling means for receiving the directionallytransferred light energy and delivering the light energy to atransducer. Preferably, the coupling means comprises an optical fiber ora waveguide; preferably, the conversion means comprises a phycobilisome.

[0015] In yet another embodiment, this invention provides anenvironmentally responsive optical sensor comprising conversion meansfor receiving ultraviolet or visible light and directionallytransferring light energy of this light, such that transfer of lightenergy is dependent on an environmental condition; and sensor means forreceiving the directionally transferred light energy and producing anindication of the environmental condition. In particular, one or moreenvironmental conditions may affect a characteristic of the transferredlight energy, such as the energy level of transferred light energy. In apreferred mode of this embodiment, the directionally transferred lightenergy comprises a photon of a particular energy level, the energy levelbeing dependent upon the environmental condition. More preferably, theconversion means comprises a phycobilisome.

[0016] In still another embodiment, this invention provides a system forprocessing a light signal comprising conversion means for receivingultraviolet or visible light and directionally transferring light energyof this light; and processing means for receiving and processing thedirectionally transferred light energy. In a preferred mode of thisembodiment, the processing means comprises an optical fiber operative totransmit the light signal and/or a photosensor. Preferably, thedirectionally transferred light energy comprises a photon, and/or theconversion means comprises a phycobilisome.

[0017] In yet another embodiment, this invention provides a method forperforming a specific binding assay comprising contacting a samplecomprising an analyte with a specific binding partner; determining theamount of the analyte present in the sample by means of its ability tospecifically bind to the specific binding partner, where a component ofthe assay is detectably labeled with a signal-generating systemcomprising phycobilisomes, the phycobilisomes being self-assemblingcomplexes of phycobiliproteins and linker proteins, where eachphycobilisome comprises at least one rod. The detectably-labeled assaycomponent is selected from the group consisting of a specific bindingpartner of the analyte, reagent molecules having the same chemicalidentity as the analyte, and reagent molecules which compete with theanalyte for specific binding to the specific binding partner. Typically,the competitive reagent molecules will have the same binding specificityas the analyte, and optionally they may have similar affinity for thespecific binding partner. In a preferred mode of this embodiment, theanalyte or its specific binding partner is attached to a solid phase.The solid phase may be, for example, a synthetic membrane, a polymer, amicroparticle, silicon, or glass, and the analyte may be, for example, anucleic acid, a drug, a ligand, an antigen, a hapten, an antibody, or acarbohydrate.

[0018] These and other embodiments of the invention provide the art withan extremely sensitive, nonisotopic detection means for assayinganalytes and for sensing molecular events and environmental conditions.Unlike enzymatic labels, phycobilisomes can be quantitatively detectedwithout accessory substrates, chromogens, cofactors, or timedincubations. Alternatively, phycobilisomes can be functionally coupledto enzymes or other signal-generating molecules to amplify or transducemolecular events, thereby generating a more preferred assay signal ortransducer output.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0019] Phycobilisomes provide labels of high sensitivity due inter aliato their extremely large molecular weights, extinction coefficients, andenergy transfer efficiencies, as well as to the high quantum yields ofconstituent phycobiliproteins. Directional energy transfer withinphycobilisomes occurs from one or more “sensitizing species” to aterminal acceptor. A sensitizing species is a first fluorophor having anemission peak capable of exciting a second (“acceptor” or “emitter”)fluorophor. Such energy transfer has application in homogeneous specificbinding assays and in transducers comprising immobilized phycobilisomes.

[0020] It is a discovery of the present invention that phycobilisomescan be stabilized, conjugated, and/or modified so that they can be usedintact in a variety of assays and formats. Among other things, thisinvention provides homogeneous preparations of isolated, soluble,stabilized phycobilisomes. Phycobilisomes may be isolated from theproducing organisms after being stabilized in situ prior to celldisruption or in membrane-bound form following cell disruption.Alternatively, phycobilisomes may be isolated intact prior to in vitrostabilization or conjugation or immobilization. In yet another mode ofoperation, phycobiliproteins and linker proteins can be isolated andreconstituted in vitro to form phycobilisomes.

[0021] Phycobilisomes and phycobilisome complexes of the invention maybe structurally stabilized to ensure that constituent phycobiliproteins,linker polypeptides and specifically bound components remain physicallyattached to one another throughout preparation and use. For applicationsrequiring intra-phycobilisome energy transfer among constituentphycobiliproteins, this invention provides internally coupledphycobilisomes, prepared by stabilization methods that preserveinter-subunit energy transfer. Such internally coupled phycobilisomesmay be detected by fluorescent, optoelectronic, piezoelectric,photometric, spectroscopic or visual means, among others. Structurallystabilized phycobilisomes which are not internally coupled are stilluseful as labels in specific binding assays, even though they do notprovide the large Stokes shift, directional energy transfer orextraordinary fluorescence intensity of internally coupledphycobilisomes. Uncoupled phycobilisomes are primarily used as labels influorescent, photometric, spectroscopic, piezoelectric or visual-readassays or, alternatively, as high molecular weight scaffolds forattachment of signal-generating molecules (e.g., enzymes, fluorophores,luminescent or electroactive compounds) that can be detected byalternative (e.g., enzymatic, fluorescent, luminescent, optoelectric orelectrochemical) means.

[0022] Definitions

[0023] The term “phycobilisome” as used herein means a supramolecularlight-absorbing structure comprising at least onephycobiliprotein-containing rod and includes phycobilisomes;phycobilisome subassemblies; rod or core fractions; uncoupled,functionally altered or damaged phycobilisomes; genetically, physically,environmentally or chemically modified phycobilisomes; chromaticallyadapted phycobilisomes; isolated or partially isolated phycobilisomes;dissociated or partially dissociated phycobilisomes; reconstituted orrearranged or recombinant or hybrid phycobilisomes. Phycobilisomes ascontemplated by the present invention contain two or morephycobiliproteins specifically connected by one or more linkerpolypeptides, where the two or more phycobiliproteins are in aparticular orientation dictated by the linker polypeptide, with theorientation typically facilitating energy transfer between thephycobiliproteins. The “linker polypeptides” affect the phycobilisomesin a number of ways. First, phycobilisome linker polypeptides candetermine the aggregation state and geometry of the particularbiliproteins with which they interact. Second, they modulate thespectroscopic properties of the biliprotein. Third, they determine thelocation of the biliprotein within the phycobilisome and bridge betweenthe biliprotein subcomplexes within the intact structure. In otherwords, linker polypeptides are proteins which bind two phycobiliproteinsspecifically and, upon binding, orient the phycobiliprotiens to enhanceenergy transfer between them. Linker polypeptides also dictate thedefined and reproduce able supramolecular composition of phycobilisomes,as distinct, for example, from chemically cross-linked fluorescentpolymers of fluorescent proteins. In addition, a large linkerpolypeptide may participate both in the assembly of the phycobilisomeand in the attachment of the phycobilisome to the photosyntheticmembrane.

[0024] Under appropriate conditions (e.g., high ionic strength), amixture of isolated phycobiliproteins and linker polypeptides will formsupramolecular structures analogous to those of naturally-occurringphotosynthetic systems. Such complex structures form as a result ofself-assembly directed by the linker polypeptides. Different linkerpolypeptides determine the composition of the phycobilisome, allowingself-assembly of multiple hexamers into a phycobilisome via the linkerpolypeptides. Typical structures created by this self-assembly will beone or more peripheral rods, or a phycobilisome core complex, or acomplex of phycobiliproteins and core complex, connected by linkerpolypeptide(s). These self-assembled structures, or molecular entitieshaving the same structure obtained by other means, are phycobilisomes ascontemplated herein.

[0025] As used herein, the term “rod” means a peripheral rod or corecomplex or disc-and-core-complex or combination or subassembly having atleast two discs joined by at least one linker polypeptide or at leastone disc joined to a core complex by at least one linker polypeptide.Rods are known in the art to be stacks of multimeric phycobiliproteindiscs joined by linker polypeptides (e.g., Glazer (1985a)). The term“disc” as used herein means a multimeric phycobiliprotein assemblagethat can be reconstituted in vitro from isolated phycobiliproteinsubunits (Grossman et al. (1993)). Such discs are typically eithertrimeric (single disc) or hexameric (double disc) and can beinterconverted in vitro under suitable conditions (e.g., Glazer et al.(1971)). The core complex of a phycobilisome typically comprises atleast two hexameric discs and associated linker polypeptides.Phycobilisomes of the instant invention, comprising at least one rodwhich comprises at least two discs, preferably share the common propertyof directional energy transfer, also referred to herein as “sidedness.”

[0026] Phycobilisomes of the instant invention can be distinguished fromisolated phycobiliproteins on structural criteria. Structurally, aphycobilisome comprises at least two hexamers (3 alpha and 3 betasubunits each) of a phycobiliprotein or phycobiliproteins joined by atleast one linker polypeptide. While the phycobiliproteins R-PE and B-PEcontain a gamma subunit (denoted a “linker” by some authors), isolatedR-PE and B-PE are each distinguishable from a phycobilisome in that theyare not connected to a second hexamer through a linker polypeptide.However, when two R-PE or two B-PE hexamers are linked by the gammasubunit in the orientation found between these two phycobiliporteins innature, the resulting rod-like supramolecular entity may be considered aphycobilisome as the term is used herein. Phycobilsomes as contemplatedby this invention are also distinct from compositionally andarchitecturally heterogeneous conjugates that have been prepared bycovalently cross-linking isolated phycobiliproteins and otherpolypeptides.

[0027] While most rods in native phycobilisomes are stacks of three orfour phycobiliprotein hexameric discs, this invention also contemplatesrods with as few as two discs connected by linker polypeptide(s). Thephycobilisome core complex is made up of the phycobiliproteinallophycocyanin (APC). Phycobiliproteins of the core form rodscontaining APC which contain other linker(s) and/or modified subunits.Examples of possible phycobilisomes, as defined under the instantinvention, are APC linked to APC via linker polypeptides, APC linked toPC via linker polypeptides and PE linked to PC via linker polypeptides.Larger complexes containing additional phycobiliproteins remain withinthe definition of phycobilisomes, so long as the complex contains atleast two phycobiliproteins which are linked and positioned in thecomplex by a linker polypeptide. Preferably, phycobilisomes of thisinvention will have at least three phycobiliprotein hexamers, and morepreferably, the phycobilisomes of this invention will have at least thenumber of phycobiliproteins found in a single rod in nature or in thecore complex.

[0028] “Stabilized phycobilisomes” are stable even under conditions ofdilute ionic strength (<0.5 M) and protein concentration (<1 mg/ml), incontrast with native phycobilisomes. In addition, they are stable in thepresence of glycerol, sucrose, and polyethylene glycol. Typically, thephycobilisomes are stabilized by means of a gentle crosslinkingtreatment, such as with formaldehyde or very low concentrations ofglutaraldehyde. Other medium-, short- or zero-length crosslinkingreagents may also be used.

[0029] Stabilized phycobilisomes that resist dissociation in dilutesolution (<1 mg/ml protein) and low ionic strength buffers (<0.5 M) butare not energetically coupled (i.e., do not exhibit intra-phycobilisomeenergy transfer) may be used for embodiments of the invention which donot require internal energy transfer (i.e., internal coupling) betweenconstituent phycobiliproteins, such as fluorescent, photometric orvisual-read specific binding assays relying on the high molar extinctioncoefficient of phycobilisome labels. Excitation of the sensitizingphycobiliproteins of a structurally stabilized, energetically uncoupledphycobilisome does not lead to a major emission peak by the terminalacceptor. Stabilized phycobilisomes which retain the property ofinter-phycobiliprotein energy transfer, by contrast, are referred to as“internally coupled phycobilisomes” and considered to be “functionallyintact.” Phycobilisomes which are functionally intact have a majoremission peak at the wavelength of the terminal acceptor.

[0030] It will be understood to those of skill in the art that theextremely effective and efficient light-harvesting properties ofinternally coupled phycobilisomes provide distinct advantages forapplications requiring highly sensitive detection and/or efficientsignal transduction. It will also be apparent to the skilled artisanfrom the instant disclosure that structurally stabilized phycobilisomeswhich are internally uncoupled are suitable for certain applicationsdescribed herein (e.g., Assay Example 1 (photometric immunoassay); AssayExample 5 (visual microliter immunoassay); and Assay Example 6(immunochromatographic dipstick)). Other applications involving energytransduction and/or biotransducers (e.g., Energy Transduction Examples 1and 2), may use either phycobilisomes that are internally coupled or,alternatively, structurally stabilized, internally uncoupledphycobilisomes which are conjugated to other molecular species (e.g.,signal-generating molecules.)

[0031] “Isolated phycobilisomes” according to this invention arephycobilisomes that are not complexed to an intact thylakoid membrane.Phycobilisomes may be solubilized from thylakoid membranes by treatmentwith surfactants, detergents, lipids, phospholipids and otheramphipathic molecules well-known in the art. Isolated phycobilisomes maybe complexed to photosystem complexes which may in turn contain athylakoid fragment, but when the isolated phycobilisomes of thisinvention are complexed to membrane structures, the membrane structuresdiffer from naturally occurring thylakoid membranes in at least onecharacteristic. Typically a membrane-bound isolated phycobilisome willbe complexed to a membrane structure that has been physically orchemically disrupted, e.g., by sonication or detergent treatment.Preferably, isolated phycobilisomes are stabilized, so that thephycobilisome resists dissociation in solutions of low ionic strength.

[0032] “Homogeneous preparations of isolated, soluble, stabilizedphycobilisomes” according to this invention demonstrate homogeneity bylack of settling within a 24-hour incubation at 1×g. Solubility can beassessed by centrifugation. “Soluble phycobilisome preparation” meansthat upon centrifugation at 1,000×g for 5 minutes, greater than 55% ofthe phycobilisomes remain in the supernatant. It is desirable thatgreater than 65%, 75%, 85%, and even 90% of the phycobilisomes remain inthe supernatant after such centrifugation, and such levels are possibleusing the methods of the present invention.

[0033] For the purpose of this invention, a “phycobilisome complex” is asupramolecular species of defined composition containing at least oneisolated phycobilisome as defined above, the isolated phycobilisomefurther being specifically bound to at least one additional component.Typically, a phycobilisome complex will include more than one additionalcomponent, and may contain more than one phycobilisome. The termphycobilisome complex includes phycobilisome complexes containing,attached to, or capable of attaching to a second photosyntheticstructure (e.g., an anchor polypeptide, a reaction center, aphotosystem, a light-harvesting complex, a membrane protein or amembrane lipid). Further, a molecular species, which may be a ligand, areceptor or a signal-generating species, can be conjugated to the secondphotosynthetic structure. For example, photosystem II may be part of aphycobilisome complex and also serve as a site for conjugation of aligand, receptor or signal-generating molecule.

[0034] The phycobilisome complex may or may not be soluble. Stabilizedphycobilisome complexes comprising thylakoid membrane-associatedconstituents (e.g., a reaction center, photosystem light-harvestingcomplex, membrane protein or membrane lipid) may be insoluble in aqueousbuffers and may be solubilized by treatment with surfactants,detergents, lipids, phospholipids and other amphipathic moleculeswell-known in the art. A phycobilisome complex may also be immobilizedto a manufactured solid support.

[0035] The term “ligand” means any substance capable of specificallybinding to a receptor. Ligands include but are not limited to agonists,antagonists, biotin (or derivatives, such as amino-biotin, imino-biotin,and diamino-biotin), haptens, antigens, carbohydrates, drugs, hormones,transmitters, cofactors, vitamins, toxins, oligonucleotides, nucleicacids, aptamers, and conjugates formed by attaching any of thesemolecules to a second molecule. The term “receptor” means any substancecapable of specifically binding to a ligand. Receptors include but arenot limited to antibodies, antibody fragments, antibody mimetics,molecular mimics and molecular imprints, molecular recognition units,adhesion molecules, soluble receptors, avidin, streptavidin, lectins,selectins, oligonucleotides, nucleic acids, membrane receptors, cellularreceptors, and drug receptors. The terms “specifically bind,”“specifically bound” and “specific binding” refer to the saturable,noncovalent interaction between a ligand and a receptor which is wellknown in the art and explicitly includes nucleic acid hybridization.“Hybridization” refers to specific binding between two or more nucleicacid sequences through complementary base pairing. Such binding is alsoreferred to as Watson-Crick base pairing. For hybridization, asufficient degree of complementarity is required to yield reversiblebinding between two selected nucleic acid sequences. Perfectcomplementarity is not required and may not be preferred for embodimentsrelying on reversibility, such as dissociation of a hybridized nucleicacid probe reagent by a target sequence.

[0036] “Signal-generating molecule” as used herein means any substancecapable of generating a detectable signal or enhancing or modulating thedetectability of a phycobilisome or transducing a phycobilisome signalinto a qualitatively or quantitatively different signal or differentform of energy. “Enhancing or modulating phycobilisome detectability”means the signal-generating molecule has an effect on phycobilisomesize, shape, charge, chemical composition or spectral properties or thatthe phycobilisome-signal-generating molecule conjugate has differentspectral properties from the unconjugated phycobilisome. “Transducingthe phycobilisome signal” means the conjugate absorbs or emits in adifferent region of the electromagnetic spectrum from the unconjugatedphycobilisome or the conjugate manifests an energy or function differentfrom the unconjugated phycobilisome, such as an electric or chemicalpotential or catalytic activity or thermal gradient or mechanical force.Signal-generating molecules as contemplated herein include, but are notlimited to, signal-generating systems comprising phycobiliproteins, dyemolecules, colloids, fluorophores and other photoactive molecules,enzymes, coenzymes, cofactors, catalytic antibodies, ribozymes, andother catalytic molecules, molecular mimics, luminescent compounds,oxidizing and reducing compounds and other electroactive molecules,photosystem molecules and reaction centers not attached tophycobilisomes in nature such as artificial reaction centers, optionallyincluding organizational, scaffold and coupling molecules used tocapture energy in artificial photosynthesis, and even otherphycobilisomes.

[0037] “Molecular mimics” and “mimetics” are synthetic molecules orgroups of molecules designed or selected to perform an equivalent orsimilar function to that of a naturally occurring or biological moleculeor group of molecules. “Artificial photosynthesis” refers to syntheticenergy conversion systems that mimic the natural process ofphotosynthesis. “Artificial reaction center” means a molecule or groupof molecules capable of existing in a light-induced charge-separatedstate, thereby mimicking the function of a reaction center. Examples ofartificial reaction centers are well-known in the art (Gust, et al.(1993), “Molecular mimicry of photosynthetic energy and electrontrasfer,” Accounts of Chemical Research, 26:198-205; Gust, et al.(1994), “Photosynthesis mimics as molecular electronic devices,” IEEE.Eng. Med. Biol., 13:58-66, and references therein). “Reaction center”means a natural photosynthetic molecule or group of molecules in whichphotoinitiated electron transfer culminates in a relatively long-lived,charge-separated state. The term “photosystem” as used herein means aphotosynthetic molecule or group of molecules that serves as afunctionally coupled energy transfer acceptor from a reaction center,for example, photosystem I or photosystem II.

[0038] “Light energy” as defined herein is a discrete energy packet thatwas originally resident in a photon; light energy as contemplated hereinmay be transformed into other energy forms. Typically, the photon (andits light energy) will be absorbed by a pigmented substance. The lightenergy from the photon may be subsequently transferred from theabsorbing species radiatively by photon emission, or the light energymay be non-radiatively transferred to an acceptor species.

[0039] Efficient signal or energy transduction (i.e., transfer of lightenergy) between a phycobilisome and an attached signal-generatingmolecule requires functional coupling between the two species.“Functional coupling” means that two processes are connected by a commonintermediate or that two species or substances participate as donor andacceptor in the transfer of mass or energy, e.g., photons or electronsor chemical or mechanical or thermal energy. The term “functionallycoupled” means that a first species, substance or process is connectedto a second species, substance or process by a common intermediate or bytransfer of a photon, electron, property, activity, mass or energy froma donor to an acceptor. Such coupling is well known in the art(Cubicciotti, R. (1993) DNA chips. “Medical & Healthcare MarketplaceGuide.” MLR Biomedical Information Services, 9th Edition, pp. 113-115;Cubicciotti, R. S. (1995) “Nucleotide-directed assembly of bimolecularand multimolecular drugs and devices.” WIPO International PublicationNo. WO 95/16788, p. 24; Gust et al. (1993), Sheeler, P. and Bianchi, D E(1983) “Cell Biology: Structure, Biochemistry, and Function”, p. 203,John Wiley & Sons, Inc., New York; Saier, H S Jr. (1987), “Enzymes inMetabolic Pathways: A comparative Study of Mechanism, Structure,Evolution, and Control”, pp. 48-59 and 132-136, Harper & Row Publishers,New York; Aidley D. J. (1989), The Physiology of Excitable Cells, ThirdEdition, p. 320, Cambridge University Press, Cambridge; Bray, HG andWhite, K (1957); Kinetics and Thermodynamics in Biochemistry, p. 135,Academic Press, New York; and Guyton, A C (1971) Textbook of MedicalPhysiology, Fourth Edition, p. 786, W. B. Saunders Company,Philadelphia). Examples of such coupling are described by Cubicciotti(1995) to include, for example:

[0040] . . . coupling proteins to selectively or actively transport ionsand metabolites; coupling cytochromes to transduce chemical energy bymeans of electron transfer-dependent oxidation-reduction reactions;coupling redox mediators such as ubiquinones, ferricinium salts,rubidium, viologens, tetrathiofulvalene, tetracyanoquinidodimethane,N-methylphenazinium, benzoquinone or conducting polymers or organicconducting salts to transfer electrons between electroactive moleculessuch as redox enzymes and electrodes in bioelectronic and optoelectronicdevices such as biosensors and biochips; coupling photoactive compoundssuch as fluorophores with other photoactive compounds or with redoxproteins or enzymes for energy transfer devices and artificialphotosynthetic systems; and coupling pro-drugs for staged-delivery ortriggered activation.

[0041] Phycobilisomes are said to be functionally coupled to a secondmolecular species or a device (e.g., a transducer) when a photon,electron, property, activity, mass or energy of a first molecule,complex or device comprising the phycobilisome is transferred to or froma second molecule, complex or device. For certain functionally coupledconjugate and biotransducer embodiments, particularly those involvingphycobilisomes, artificial reaction centers and electronic transducers,electronic coupling is preferred. “Electronic coupling” as used hereinincludes single-electron transfer and coupling mediated by direct,through-space overlap of the relevant orbitals of the donor(s) andacceptor and by through-bond superexchange(s) and may occur bysingle-step or multistep processes within a molecule or betweenmolecules positioned by covalent bonding or noncovalent interaction(s).

[0042] Based on the foregoing definitions, it will be apparent to one ofskill in the art that a ligand, receptor or signal-generating moleculeattached to a phycobilisome can further be functionally coupled to thephycobilisome, and that functional coupling includes the exchange ortransfer of mass or energy between a phycobilisome and an attachedspecies. Functional coupling does not require direct attachment of asignal-generating molecule to a phycobilisome. A phycobilisome can befunctionally coupled to a second molecule or complex or device orprocess indirectly, e.g., through a specific binding reaction between anattached ligand or receptor and a specific binding partner comprising asignal-generating molecule.

[0043] The term “manufactured solid support” as used herein means anystructure, device, matrix or membrane which is not the native attachmentsite for phycobilisomes and includes non-thylakoid biological membranesand synthetic and biomimetic membranes which may comprise peptides,proteins and/or other ligands and receptors. Non-thylakoid, syntheticand biomimetic membranes can either be used directly as solid supports,or attached to or deposited or prepared on solid supports, to facilitateself-assembly, reconstitution and/or immobilization of phycobilisomes,phycobilisome subassemblies and conjugates via covalent or non-covalentattachment. In addition, phycobilisome complexes of the inventioncomprising thylakoid membrane fragments or constituents (e.g., lipids,proteins and membrane receptors) may be immobilized to a manufacturedsolid support.

[0044] The term “biotransducer” as used herein means biological orbiomimetic molecule(s) immobilized at and/or functionally coupled to atransducer. “Biological or biomimetic” molecule(s) may be isolated frombiological sources or produced synthetically or may perform a functionequivalent to biological molecule(s), e.g., immunologic recognition,nucleic acid hybridization, enzymatic catalysis, photosynthesis or acomponent reaction of photosynthesis. “Phycobilisome-basedbiotransducer” means a biotransducer comprising a phycobilisome orphycobilisome complex, wherein the phycobilisome and transducer elementsare necessary and functionally inseparable components of a product orsystem which performs a useful function. Where an instrument or device(e.g., a microscope, fluorometer, spectrofluorometer or Clark electrode)merely performs the function of measuring a property or activity of aphycobilisome or phycobilisome preparation (e.g., size, fluorescence,absorbance or rate of oxygen evolution), the instrument is not aphycobilisome-based biotransducer, because the phycobilisome is not acomponent of the measuring device. Instead, in such an instance thephycobilisome or phycobilisome preparation is the object of measurementor the sample to be measured and is both structurally and functionallyunnecessary to and separable from the product that performs themeasurement. By contrast, the phycobilisome of a phycobilisome-basedbiotransducer is operatively associated with, attached to, immobilizedat, packaged with, or otherwise structurally or functionally inseparablefrom the transducer. A phycobilisome-based biotransducer can, of course,be a two-component (or multi-component) product or system comprising atransducer component and a disposable, replaceable, reusable orupgradeable phycobilisome-containing cartridge, module, slide, disk,film, layer, fiber, connector, attachment or part that serves as aninterface between the phycobilisome and the transducer. In such a case,the phycobilisome-containing component is physically separable from thetransducer component but must be inserted, attached, rejoined orreplaced to form the functionally coupled two-component system capableof performing the intended function. The “functionally coupled”transducer converts an activity, energy or property of the biological orbiomimetic molecule(s) (e.g., the phycobilisome(s) or phycobilisomeconjugate(s)) to useful work or information or a detectable signal.

[0045] Preparation of Modified Phycobilisomes

[0046] Phycobilisome Isolation

[0047] Phycobilisomes, according to the present invention, areself-assembling complexes of phycobiliproteins and linker proteinscomprising at least one rod. The phycobilisomes of the present inventionmay be obtained from either prokaryotic cyanobacteria (blue-green algae)or eukaryotic red algae. The algae may be wild-type, mutants, hybrids,or genetic recombinants capable of expressing phycobilisomeconstituents. The algae may be harvested from natural environments (thewild) or grown under artificially controlled conditions. Such artificialconditions may simulate a natural environment or they may be designed toinduce chromatic adaption, for example, to modulate the composition ofphycobilisomes. Artificial conditions may support either autotrophic,mixotrophic, or heterotrophic growth.

[0048] General procedures for isolation of phycobilisomes from a widerange of unicellular algae have been described (see, e.g., Gantt et al.(1979) Plant Physiol. 63:615-620). Phycobilisomes can be isolated fromred algae (e.g., Porphyridium cruentum) and blue-green algae (e.g.,Anabaena variabilis, Spirulina platensis) by methods modified from thoseof Gantt and Lipschultz (1972) J. Cell Biol. 54:313-324. Typically,algal or cyanobacterial cells grown under conditions which elicitproduction of the photosynthetic apparatus in the cells are lysed in aphosphate buffered detergent solution. After removing cellular debris,phycobilisomes may be isolated from the aqueous supernatant by gradientcentrifugation or precipitation with high concentrations of phosphatebuffer (≦1 M) or polyols (e.g., sucrose or polyethylene glycol).Isolated phycobilisomes are redissolved in phosphate buffer (about0.75M). Exemplary procedures are shown below.

[0049] Exemplary Procedure 1. Isolation of Phycobilisomes from Red andBlue-Green Algae by Gradient Ultracentrifugation

[0050] Freshly cultured or frozen (−20° C. or −70° C.) algae can becultured autotrophically in 40-500 L stirred tanks with continuousfluorescent illumination and harvested by centrifugation. Porphyridiumcruentum (P. cruentum) can be grown at 20-22° C. in an artificialseawater medium (pH 8.0) comprising sodium salts, Tadros Metals, InstantOcean and Dunaliella vitamins. Anabaena variabilis can be grown at 25°C. in double-strength BG-11 medium containing sodium and potassiumsalts, magnesium sulfate, calcium chloride, citric acid, ferric ammoniumcitrate and A5 Metals (pH 7.8).

[0051] Unless otherwise specified, all preparative steps can beperformed at room temperature (20-23° C) in 0.75 M potassium phosphate(pH 7.0-7.2) optionally containing 0.05% sodium azide (KPi buffer).Twenty-four grams (wet weight) of packed cells are resuspended in 48 mlKPi buffer. PMSF (1 mM), benzamidine (5 mM) and DNase I (10 ul ofRNase-free stock at 10 U/ul) are then added, and the suspension ispassed four times in 15 ml increments through a French pressure cell(Aminco) operated at 1000-1250 p.s.i. TRITON X-100(t-octylphenoxypolyethoxyethanol, Rohm and Haas) is added to 2% and thebroken cell mixture is stirred for 20 minutes. Particulate matter isremoved by centrifugation at 15,000 rpm for 45 minutes in a SorvallRC-5B Refrigerated Superspeed Centrifuge using an SS34 rotor. Thesupernatant is withdrawn by syringe from underneath the floatingchlorophyll fraction, and approximately 9 ml is layered on each of sixbuffered sucrose step gradients comprising (from bottom to top) 2 Msucrose (4 ml), 1 M sucrose (8 ml), 0.5 M sucrose (7 ml) and 0.25 Msucrose (7 ml), all in 0.75 M KPi. Gradients are centrifuged 12-18 hoursat 25,000 rpm in an SW27 rotor. Following centrifugation, green, brown,brown-red, purple-red, purple and clear layers (top to bottom) can bediscerned with varying resolution. Only the purple-red (rods andphycobiliprotein aggregates) and purple (phycobilisome) bands areretained. Purple-red bands are withdrawn by suction using a pasteurpipet, pooled and stored at 2-8° C. Stabilized and conjugated rods maybe prepared from this fraction, purified by gel chromatography, andimmobilized. Purple phycobilisome bands in the 1.0 M sucrose layer arewithdrawn, pooled, diluted four-fold with KPi buffer and centrifuged at15,000 rpm for 40 minutes in an SS34 rotor. Resultant supernatants arewithdrawn from pelleted sediment (if any) and centrifuged at 30,000 rpmfor two hours in a VTi50 rotor. Final supernatants are quickly andcarefully aspirated, and phycobilisome-containing pellets areresuspended in a minimal volume of KPi buffer. Protein concentration canbe determined by the method of Lowry et al. (1951 J. Biol. Chem.,193:265-275). Protein measurements are carried out with the Folin phenolreagent using bovine serum albumin as standard with suitable controlsfor sucrose and TRITON X-100 interference. Absorption spectra weremeasured with a Shimadzu Model UV-160 recording spectrophotometer.Fluorescence spectra were recorded at room temperature in a 4 ml quartzcuvette with a SPEX FLUOROMAX™ (scanning excitation/emissionfluorometer) coupled to a Compudyne PC. In general, phycobilisomeemission spectra can be obtained by exciting phycobilisomes using fightof wavelengths within the absorption spectrum of the distal sensitizingphycobiliprotein (e.g., 545 nm for P. cruentum B-PE). Phycobilisomes canbe routinely characterized by 1) peak absorption per mg protein (e.g.,AU₅₄₅/mg for P. cruentum), 2) fluorescence signal per definedconcentration (e.g., cps at Emax for intact phycobilisomes at 10 ng/ml),and 3) one or more fluorescence ratios reflecting the efficiency ofinter-phycobiliprotein energy transfer (e.g., 666/573 nm emission for P.cruentum as an index of APC/B-PE coupling). Up to 24 grams wet weight ofbiomass can be conveniently handled using six 35 ml centrifuge tubes inan SW27 rotor for the final sucrose gradient ultracentrifugation step.Phycobilisome recovery is on the order of 0.1-1.0% of initial biomass.

[0052] Exemplary Procedure 2. Large-Scale Isolation of PhycobilisomesWithout Gradient Ultracentrifugation

[0053] The convenience, scale and cost-effectiveness of phycobilisomeisolation by conventional methods (e.g., Gantt and Lipschultz (1972)supra, Gantt et al. (1979) supra) are severely limited by the need forgradient ultracentrifugation. To enable scalable and economicalproduction of phycobilisomes, procedures were developed for isolatingphycobilisomes from different organisms without gradientultracentrifugation. Methods based on those for Anabaena variabilisusing TRITON X-100 solubilization and PEG precipitation failed to yieldintact phycobilisomes from some organisms, notably P. cruentum. Anadditional treatment step is required to protect P. cruentumphycobilisomes during removal of Triton X-100 and PEG. Either sucrose orformaldehyde treatment was found to be effective. Summarized below isthe sucrose treatment procedure, which has been validated withmodification for both rhodophytes (e.g., P. cruentum) and cyanophytes(e.g., Anabaena variabilis, Spirulina platensis). Preparative scale canbe readily varied by selecting different centrifuge and rotorcombinations and adjusting volumes accordingly.

[0054] Cells are suspended in 5 ml 0.75 M KPi (pH 6.8) per gram wetweight. PMSF and benzamidine are added to a final concentration of 1 mMand 5 mM, respectively, and the suspension is passed through a Frenchpressure cell three times at 1000-1250 p.s.i. Membrane-associatedphycobilisomes are solubilized by treatment with 2% TRITON X-100 in 0.75M KPi (pH 6.8) for 20 minutes with stirring. The broken cell preparationis centrifuged at 15,000 rpm for 20 minutes in a Sorvall RC-5BRefrigerated Superspeed Centrifuge using an SS34 rotor to removemembrane fragments and particulate debris. The supernatant is collectedby suction from underneath the floating chlorophyll layer. The pellet isdiscarded. Polyethylene glycol 8000 is added to the supernatant to aconcentration of 15% (wt/vol). The mixture is stirred for one hour andcentrifuged for 20 minutes at 15,000 rpm in an SS34 rotor. Thesupernatant is discarded. The pellet is resuspended by addition of 2 Msucrose in 0.75 M KPi with gentle vortexing to a final concentration of1.5 M sucrose. Thirty minutes following sucrose addition, the suspensionis diluted approximately 4-fold with 0.75 M KPi (pH 6.8) and centrifugedfor three hours at 40,000 rpm (20° C.) in a Beckman L8-M Ultracentrifugeusing a VTi50 rotor. The supernatant is discarded. The pellet isresuspended in a minimal volume of 0.75 M KPi (pH 6.8), characterized byprotein, absorption and fluorescence measurements (cf. supra) and storedeither refrigerated or at ambient temperature, depending on the sourceof phycobilisomes.

[0055] Exemplary Procedure 3. Large-Scale Preparation of Phycobilisomesfrom Algae

[0056] An alternative large-scale isolation procedure described byGrossman and Brand (1983, Carnegie Institution of Washington Yearbook,82, 116-120) can also be used to prepare phycobilisomes. While thisprocedure has not been widely used due to the requirement forlarge-scale preparative centrifugation, it can be adapted to a suitablescale using appropriately sized centrifuge tubes. This procedure, calledthe “rapid pelleting method” by the authors, involves breaking the cellsin 1 M phosphate buffer by passing cells through a French pressure cell.The lysate is brought to 1% TRITON X-100, incubated at room temperaturefor 30 min, then centrifuged at 32,000×g for 30 min. With laboratoryscale preparative centrifuges (e.g., Sorval RC-5A), this is done in verysmall centrifuge tubes (e.g., using the SS34 rotor the tubes are about45 mL with 8 places giving about 300 mL useful volume per centrifugationrun). The pellet is resuspended in 0.6 M phosphate buffer (pH 7.5) andhomogenized in a glass homogenizer. TRITON X-100 is added to 1% andincubated for 30 min at room temperature. The solution is againcentrifuged at 32,000×g for 30 min. A large amount of the 10phycobilisome then remains in solution, so the pellet is discarded. Thesupernatant is diluted 10-fold with 1.0 M NaKPO₄ (pH 7.5) andcentrifuged at 32,000×g for 1 h to bring down the phycobilisomes. Thismethod has been applied to various algal phycobilisomes (e.g., Anacystisnidulans, Porphyridium aerugineum, Cyanidium caldarium) from a diversegroup of algae (Grossman and Brand (1983) Carnegie Institution ofWashington Yearbook 82, 116-120) and can be adapted for phycobilisomepreparation from many species.

[0057] Exemplary Procedure 4. Preparation of Phycobilisomes fromCyanobacteria

[0058] Another alternative isolation procedure has been described forpreparation of cyanobacterial phycobilisomes (Siegelman and Kycia (1982)Plant Physiol., 70:887-897). Phycobilisomes containing phycoerythrin canbe isolated in the following way. Cells are lysed in a 1.0 M potassiumphosphate buffer (pH 6.8) containing 1% TRITON X-100 by stirring for 1to 1.5 h at room temperature. The suspension is centrifuged at low speedand the supernatant discarded. The pellet is resuspended in 0.5 Mpotassium phosphate (pH 6.8) containing 1% TRITON X-100 and centrifugedfor 5 min. The supernatant containing the phycobilisomes is removed sothat the chlorophyll fraction is left in the tube. The solubilizedphycobilisomes are precipitated by addition of solid potassium phosphate(at a 1: 1 ratio of dibasic and monobasic forms) to a finalconcentration of 1.5 M at pH 6.8. This is centrifuged for 10 min and theclear supernatant removed from the soft pellet containing thephycobilisomes. The phycobilisome pellet is suspended in 0.5 M potassiumphosphate (pH 6.8) with 1% TRITON X-100 and precipitated again. Thetwice precipitated phycobilisomes are resuspended in 1.25 M potassiumphosphate (pH 6.8) and stored frozen. Phycobilisomes containing nophycoerythrin can also be isolated with minimal changes to the aboveprocedure, the changes consisting essentially of increasing the amountof potassium phosphate used to precipitate the phycobilisomes from 1.0 Mto 1.25 M in several of the steps. With other minimal modifications,this method may be applied to red algae such as P. cruentum.

[0059] Stabilization of Phycobilisomes

[0060] In agreement with published studies (e.g., Katoh (1988)Phycobilisome stability, in Methods in Enzymology Vol. 167, pp. 313-318,Academic Press; and Gantt et al., 1979, supra), isolated phycobilisomeswere shown to be unstable to decreases in protein concentration andionic strength. Using P. cruentum phycobilisomes, for example,intra-phycobilisome energy transfer was disrupted within minutesfollowing dilution of protein (below about 1 mg/ml) or buffer (belowabout 0.5 M KPi), as exhibited by concentration-dependent decreases inthe ratio of 666/573 nm fluorescence emission with 545 nm excitation.Similar dissociation was observed for phycobilisomes isolated fromSpirulina platensis and Anabaena variabilis based on a decrease inemission of the terminal acceptor. To enable reproducible preparation ofstable phycobilisome-labeled ligands and receptors for use inconventional specific binding assay configurations, phycobilisomes arepreferably stabilized against dissociation.

[0061] Stabilization methods which are embraced by the present inventioninclude covalent as well as non-covalent means. Covalent methods includecrosslinking and multi-point attachment of polymers that span at leasttwo phycobilisome constituent proteins. Crosslinking agents may bezero-length (involving the direct attachment of two phycobilisome groupswithout intervening spacer atoms) or they may include spacer arms ofvarying length. Non-covalent stabilization may be accomplished usingcosolvents, such as salts and sugars, hydrophobic or affinity-basedinteractions, such as with certain polymers or polyvalent receptors,entrapment or encapsulation (e.g., using gels, liposomes, or micelles),or changes in physical state, such as freezing or dehydrating. Suitablemethods for stabilizing phycobilisomes include the methods discussedbelow.

[0062] (1) Covalent stabilization can be accomplished byintra-phycobilisome (inter-subunit) crosslinking, preferably through useof short- or zero-length bifunctional reagents well-known in the art ofprotein modification (e.g., Wong (1991) Chemistry of Protein Conjugationand Crosslinking, CRC Press).

[0063] (2) Covalent stabilization can also be achieved by multi-siteattachment of natural or synthetic polymers such as carbohydrates,lipids, oligonucleotides, proteins, peptides, polyamino acids, random orordered copolymers of amino acids, nucleosides, sugars or other smallorganic molecules. This method for covalent interconnection ofphycobilisome subunits can be performed using either one-step ortwo-step techniques. In the preferred two-step approach, a firstreactant (either the phycobilisome or the bridging polymer) is activatedin step one. Following removal of excess reagent, the activated reactantis attached in step two to functional groups on the second reactant.

[0064] (3) Non-covalent stabilization can be achieved using cosolvents,detergents or other buffer additives that render phycobilisomedissociation thermodynamically unfavorable. In a particular embodiment,phycobilisomes are encapsulated by sonication to form vesiclescontaining the phycobilisomes in a solution which promotes non-covalentstabilization (e.g., 0.75 M phosphate buffer). Suitable materials forformation of liposomes around a stabilizing solution of phycobilisomesmay be readily selected by the skilled worker (see discussion ofimmobilization to liposomes below). Ligands or receptors or othersuitable molecular species may be introduced into the liposome membrane,as is well known in the art, thereby conferring specific bindingproperties on the encapsulated phycobilisomes. (4) Non-covalent,affinity-based stabilization can also be accomplished using molecules orgroups of molecules having a finite affinity for functional bindingsites spanning at least two phycobilisome subunits. Molecules havingsuitable affinity may be selected by screening or combinatorial methodsfrom groups such as naturally occurring, modified or syntheticantibodies or antibody fragments, oligonucleotides, peptides, proteins,lectins, carbohydrates or polymers of small organic molecules. Affinitycan be determined by binding studies, but suitable molecules may be moresimply identified by monitoring intra-phycobilisome energy transfer upondilution of the phycobiliprotein or buffer concentration.

[0065] Phycobilisomes may be isolated from the producing organisms afterbeing stabilized in situ prior to cell disruption or in membrane-boundform following cell disruption. Alternatively, phycobilisomes may beisolated intact prior to in vitro stabilization or conjugation orimmobilization. In yet another mode of operation, phycobiliproteins andlinker proteins can be isolated and reconstituted in vitro to formphycobilisomes, which are then stabilized as described herein.

[0066] In a preferred embodiment, phycobilisomes can be stabilizedthrough a one-step reaction with short to medium chain-lengthcrosslinking agents. To produce stabilized phycobilisomes that remainsoluble, reagents and reaction conditions are selected to favorintra-phycobilisome crosslinking over inter-phycobilisomepolymerization. The medium chain-length homobifunctional dialdehyde,glutaraldehyde (GA), and the short chain-length monoaldehyde,formaldehyde (FA), are both effective in protecting phycobilisomes fromdilution-induced uncoupling of energy transfer. Maximal stabilization ofphycobilisomes with GA is accompanied by partial insolubilization whichis only apparent following centrifugation or prolonged storage.GA-induced insolubilization can be minimized through co-optimization ofGA and phycobilisome concentrations, pH, buffer concentration, andreaction time. Alternatively, conditions can be adjusted to yieldGA-stabilized phycobilisomes that remain in homogeneous suspension, butsediment completely when centrifuged at 8000 g for two minutes. Thestabilizing effect of GA can be improved by sequential treatment ofphycobilisomes at low GA/phycobilisome mass ratio (e.g., 0.027%GA/0.727% phycobilisomes) followed by dilution of the reaction mixturewith buffered GA to increase the GA/phycobilisome ratio (e.g., to 0.10%GA/0.10% phycobilisomes). In contrast to GA treatment, maximallyeffective stabilization with shorter chain-length crosslinkers (e.g.,FA) can be achieved without loss of soluble phycobilisomes toaggregation or precipitation.

[0067] Isolated phycobilisomes, stabilized phycobilisomes andphycobilisome conjugates prepared from different cyanobacteria andrhodophytes were exposed to a diverse assortment of substances andconditions to identify chemical and environmental factors capable ofmodulating either the aggregation state or spectral properties of thedifferent phycobilisome preparations. Phycobilisomes diluted toconcentrations ranging from 10 ug/ml to 10 mg/ml were subjected tovarying temperatures, pressures, freeze-thaw cycles, lyophilizationconditions, light sources and exposures, mechanical shaking, sonication,ultracentrifugation, ultrafiltration, dialysis, electrophoresis, pH,ionic strength, buffers, acids, bases, chaotropic agents, sugars, salts,neutral and charged polymers, copolymers, ionic and nonionic detergents,polar and nonpolar solvents, oxidizing and reducing agents, proteinmodifying reagents and combinations of such treatments designed toreversibly modulate or irreversibly perturb the phycobilisomeaggregation state or spectral properties. For all but the most extremeinterventions (e.g., denaturing conditions), phycobilisome preparationscould be identified with varying tolerances to each type of treatment,suggesting the possibility of using selected or engineeredphycobilisomes to sense and report conditions in a particularenvironment or sample. Especially noteworthy were differences inphycobilisome fluorescent properties in dry and partially hydratedstates as a function of stabilization and storage conditions.

STABILIZATION EXAMPLE 1 Cross-Linked Phycobilisomes Tested forFunctionality

[0068] To determine effects of stabilization and conjugation procedureson the size distribution and buoyant density of phycobilisomepreparations, the behavior of reaction precursors and products wasevaluated on discontinuous sucrose gradients similar to those used forphycobilisome isolation. One-half milligram aliquots of lysine-quenched,GA-stabilized phycobilisomes, unpurified phycobilisome-antibodyconjugates and unmodified phycobilisomes were applied to 10 ml sucrosegradients comprising 2.5 ml steps of 2.0 M, 1.0 M, 0.5 M and 0.25 Msucrose in 0.75 M KPi (pH 7.35). Gradients were centrifuged 20 hours(18° C.) at 50,000 rpm in a 70.1 Ti rotor. A purple-red band (rods andB-PE aggregates) appeared in the upper half of the unmodifiedphycobilisome gradient, indicating some breakdown of nativephycobilisomes under these conditions. GA-stabilized phycobilisomes andphycobilisome-antibody conjugate gradients, by contrast, formed a singleband in the 1.5 M sucrose region. These results indicate that 1) GAtreatment successfully prevented phycobilisome dissociation duringultracentrifugation, 2) the one-step GA stabilization/conjugationprocess did not yield uncontrolled polymerization of phycobilisomes orconjugates, and 3) stabilized phycobilisomes and conjugates remainedsoluble following covalent crosslinking by methods described herein.

STABILIZATION EXAMPLE 2 Preparation of a Stable, Modified PhycobilisomeReagent Using Formaldehyde

[0069] For most uses of phycobilisomes as detection reagents, it ispreferred that they remain structurally intact (“non-dissociated”). Foruse in heterogeneous specific binding assays (in which bound and freelabeled species must be separated prior to measurement), phycobilisomesare preferably stabilized to prevent spontaneous dissociation duringconjugation, purification, assay, product manufacturing, shipping andstorage. Covalent stabilization methods of this invention can preservethe energetic coupling and/or structural integrity of phycobilisomeswithout compromising solubility. Crosslinkers were used under conditionscarefully optimized to avoid precipitation arising from uncontrolledpolymerization or charge neutralization. Key optimization parametersincluded crosslinker type and reactivity, absolute and relative reagentand phycobilisome concentrations, reaction time, pH, and methods fortermination and purification. Formaldehyde stabilization, exemplifiedusing P. cruentum phycobilisomes, was performed as follows.

[0070] Isolated phycobilisomes were adjusted to a protein concentrationof 8.0 mg/ml in 0.75 M KPi (pH 7.2) containing 0.05% sodium azide. FA(formaldehyde) (11% in 0.75 M KPi) was added dropwise with vortexing ina 10% volume to yield a final concentration of 1.0%. The reactionmixture was left standing for 18 hours at room temperature and quenchedwith 1 M L-lysine. For prolonged storage, FA-treated phycobilisomes werereduced with sodium cyanoborohydride and purified over SEPHAROSE CL-6Bequilibrated with 100 mM KPi (pH 7.2) containing 150 mM sodium chlorideand 0.05% sodium azide.

[0071] Phycobilisome susceptibility to dissociation following dilutionwas prevented by FA treatment in a time- and dose-dependent manner.Preparations treated at varying FA concentrations for 18 hours wereincubated for two hours in 0.75 M KPi (pH 7.2) at 65 ug/ml and 0.6ug/ml, respectively, prior to absorption and fluorescence measurements(545 nm excitation). Fluorescence Emission (@0.6 ug/ml) [FA] (%) AU ₅₄₅E₆₆₆ E₅₇₃ Ratio (× 18 hr) (@65 ug/ml) (cps × 10⁻⁶) (cps × 10⁻⁶)E₆₆₆/E₅₇₃ no FA (control) 0.302 1.07 1.22 0.88 0.015 0.326 1.26 1.141.11 0.05  0.359 1.38 0.63 2.19 0.15  0.338 1.43 0.40 3.58 0.50  0.3671.45 0.38 3.82 1.00  0.357 1.46 0.36 4.06

[0072] Optimal preservation of energy transfer was obtained at 1% FA.Treatment with 2% FA for five hours provided equivalent protection.

[0073] Similar FA treatment conditions were required to stabilizephycobilisomes against dissociation in reduced ionic strength buffers.FA-treated phycobilisomes were diluted to approximately 0.75 ug/ml in0.1 M KPi and left standing for 40 hours at room temperature.Fluorescence data for preparations treated with 1% FA for increasingintervals are summarized below: Fluorescence treatment (cps × 10⁻⁶ @0.75 ug/ml) Ratio time (hrs) E₆₆₆ E₅₇₃ E_(666/)E₅₇₃ 0 0.45 6.25 0.07 21.88 1.02 1.84 5 2.06 1.00 2.06 18 2.31 0.91 2.54

[0074] To determine whether the stabilizing effect of FA was accompaniedby formation of large, insoluble polymers of crosslinked phycobilisomes,FA-induced precipitation was estimated by centrifugation. Phycobilisomeswere treated with FA concentrations up to 3.0%. Reactions were leftstanding at room temperature for 2-18 hours. Recovery of soluble,modified phycobilisomes was estimated by comparing 545 nm absorbance ofthoroughly mixed preparations with supernatants obtained aftertwo-minute centrifugation at 8000×g. Relative percent precipitation wasdetermined by subtracting percent recovery of FA-treated preparationsfrom untreated controls. Only prolonged treatments with high FAconcentrations yielded significant precipitation. % recovery relative %at treatment time = precipitation at time = [FA] (%) 2 hours 5 hours 16hours 2 hours 5 hours hours 0 FA 95.7 96.0 95.4 0   0 0 control 0.5%93.5 — 97.0 2.2 — 0 1.0% 93.7 96.6 94.6 2.0 0 0.8 2.0% — 92.4 — — 3.6 —3.0% 92.0 78.6 40.1 3.7 17.4 55.3

[0075] No precipitation was observed in FA-modified phycobilisomes (2%FA×5 hours) left standing at room temperature for 18 weeks. In addition,no differences in recovery, conjugation efficiency or immunoassayperformance were apparent using FA-treated phycobilisomes prepared withand without mixing. These results indicate that FA-treated phycobilisomepreparations behaved as homogeneous solutions for purposes of proteinmodification, purification, immunoassay and prolonged storage.

[0076] FA-stabilized phycobilisomes were routinely stored at roomtemperature. Reference samples were refrigerated (2-8° C.) for stabilitycomparisons. FA-stabilized phycobilisomes were characterized byabsorption and fluorescence measurements using a Shimadzu Model UV-160recording spectrophotometer and a SPEX FLUOROMAX fluorometer,respectively.

STABILIZATION EXAMPLE 3 Preparation of a Stable, Modified PhycobilisomeReagent Using Glutaraldehyde

[0077] Phycobilisomes were adjusted to a concentration of 2-10 mg/ml,preferably about 8.0 mg/ml, with 0.75 M KPi (pH 7.3) containing 0.05%sodium azide. GA (glutaraldehyde) (0.2-1.0% in 0.75 M KPi) was addeddropwise with vortexing in a 10-50% volume over two minutes or,alternatively, in 3-6 incremental additions over elapsed periods up tothree hours. Following addition of GA, the reaction mixture was leftstanding at room temperature for 1-18 hours. In a preferredstabilization protocol designed to precede conjugation by modifiedone-step GA methods, a reaction mixture comprising 7.27 mg/mlphycobilisomes plus 0.023% GA was incubated at room temperature for 3hours before addition of a ligand (e.g., antigen) or receptor (e.g.,antibody) containing primary amines. Alternatively, the GA stabilizationreaction was terminated by addition of excess primary amines (e.g., 100mM lysine, arginine, glycine, cysteine or glutamic acid). In a preferredprotocol for GA stabilization prior to conjugation or immobilizationthrough groups other than free aldehydes, phycobilisomes (7.27 mg/ml)were first stabilized for 1-2 hours with 0.023% GA followed by a 1-4hour incubation with an additional 5-10 volumes of 0.05-0.15% GA. Thereaction was terminated by addition of 100 mM lysine, glycine, cysteine,glutamic acid or an alternative primary amine-containing quench agent.GA-stabilized phycobilisomes were characterized by absorption andfluorescence measurements in accordance with methods used for unmodifiedphycobilisomes and FA-stabilized phycobilisomes.

[0078] Stabilized phycobilisomes from P. cruentum reproducibly met thefollowing specifications: Absorptivity: >4 AU₅₄₅/mg (mean about 5.0)Fluorescence signal (666 nm): >10⁴ cps at 1 ng/ml with excitation at 545nm Fluorescence ratio: 666/573 nm emission ratio > 3.0 with excitationat 545 nm

[0079] The stabilizing effect of GA was titrated as follows. GA(0.03-3.0% in 0.75 M KPi) was added dropwise with mixing tophycobilisomes in 0.75 M KPi to yield reaction mixtures comprising 10mg/ml phycobilisomes and GA at concentrations ranging from 0.003% to0.3%. After 12 hours at room temperature, reactions were quenched with100 mM glycine and stored at room temperature for two weeks prior toevaluation.

[0080] Stability to dilution was determined by incubating resultantpreparations at 10 ug/ml for varying periods of time in 0.75 M KPi (pH7.2). Concentrated phycobilisome stocks were diluted to 10 ug/ml at timezero. Emission spectra of diluted preparations were recorded at varyingtime intervals with 545 nm excitation. Fluorescence data are expressedas E₆₆₆/E₅₇₃ ratios. Time-zero ratios (30 seconds post-dilution)averaged 2.10 for untreated controls compared to 3.21 for 0.03%GA-treated phycobilisomes, indicating significant dilution-dependentdissociation of controls within 30 seconds. Empirical Absorption: AU₅₄₅Post-dilution E₆₆₆/₅₇₃ ratio Treatment result major peaks (10 ug/ml) t =1 hr t = 18 hr change 0 GA homogeneous 545 > 565 0.052 1.04 0.70 −33%control purple liquid 0.003% GA no apparent 545 > 565 0.049 1.31 0.98−25% change  0.01% GA no apparent 545 > 350 0.051 2.05 1.72 −16% change 0.03% GA slightly hazy, 545 > 565 >350 0.055 3.04 3.01  −1% tracesettling  0.10% GA cloudy with 545 > 350 0.051 3.41 3.23  −5%aggregation  0.30% GA precipitation 550 > 350 0.003 ND ND NDdiscoloration

[0081] Stabilization to reduced ionic strength by sub-precipitatingconcentrations of GA was assessed by monitoring fluorescence spectra ofcontrol vs. 0.03% GA-treated phycobilisomes following dilution invarying mixtures of deionized water and 0.75 M KPi. The stabilizingeffect of 0.03% GA treatment was dramatically apparent within one hourof dilution: phycobilisome emission (E₆₆₆ × 10⁻⁷ cps) followingexcitation at 545 nm [KPi] (mM) Untreated GA-treated 750 1.68 1.69 2501.47 1.67 100 1.11 1.68  30 0.65 (shoulder) 1.66  10 0.50 (no peak) 1.610.75 (H₂0 diluent) 0.46 (no peak) 1.56

[0082] Details of the quench, reduction and purification steps of the GA(and FA) stabilization process were varied for different applications.Properties of aldehyde-treated phycobilisomes could be varied byquenching reactions with different amino acids (e.g., glycine,D-arginine, L-lysine). In addition, new chemical groups could beconveniently introduced by selecting suitable quench agents (e.g.,L-cysteine for introduction of thiol groups, glucosamine forintroduction of sugar groups). For example, phycobilisomes were treatedwith 0.023% GA, quenched with 10 mM L-cysteine and either stored forsubsequent use or reduced, purified and conjugated as follows.Cysteine-quenched, GA-treated phycobilisomes were reduced with 30 mMdithioerythritol and purified over SEPHAROSE™ (beaded agarose) CL-6Bequilibrated with 100 mM KPi containing 100 mM NaCl (pH 7.4).Pyridyl-derivatized streptavidin was prepared by established methodsusing SPDP in 100 MM sodium phosphate (pH 7.4) at an SPDP/streptavidinmolar ratio of 10. The product was purified by dialysis in the samebuffer and reacted with thiolated phycobilisomes atstreptavidin/phycobilisome molar ratios ranging from 2 to 10. Thethiolated phycobilisomes were added to the conjugation reactionimmediately following reduction. Streptavidin-phycobilisome conjugateswere purified over SEPHAROSE CL-6B. Biotin-specific binding wasdemonstrated using biotinylated BSA immobilized on paramagneticparticles as the capture reagent.

STABILIZATION EXAMPLE 4 Storage of Phycobilisomes and ModifiedPhycobilisomes in Dehydrated Form

[0083] Dry-reagent formats are preferred for many diagnostic tests andkits as a means of eliminating reagent addition steps, improvingreproducibility and increasing shelf-life. Lyophilization(freeze-drying) is a common method of drying reagents for long-termstorage. Literature suggests that phycobilisomes are unstable tofreezing. (See, e.g., Gantt and Lipschultz (1972), “Phycobilisomes ofPorphyridium Cruentum”, J. Cell Biol., 54:313-324; Canaani et al.(1980), “Reassembly of Phycobilisomes from Allophycocyanin and aPhycocyanin-Phycoerythrin Complex”, FEBS Letters, 115(2):225-229).Freeze-drying of phycobilisomes and conjugates was undertaken toestablish feasibility of dry-reagent phycobilisome product formats.

[0084] Phycobilisomes were isolated from P. cruentum in 0.75 M KPi at8.8-9.5 mg/ml. Three to twenty microliter aliquots (45-190 μg) wereflash-frozen and vacuum evaporated in microtiter wells. The driedphycobilisomes were stored 0-4 weeks at room temperature, resuspended,diluted, and transferred to 3 ml cuvettes for absorbance andfluorescence measurements. Phycobilisomes stored 1S in buffered solution(8.8-9.8 mg/ml in 0.75 M KPi containing 0.05% sodium azide) were used asreference.

[0085] Absorbance was not affected, while fluorescence was affectedslightly. Unmodified phycobilisomes survived freeze-drying and 4-weekstorage with no change in absorbance. There was a 15-20% decrease inboth fluorescence intensity and the 666/573 nm emission ratio withfreeze-drying and 4-week storage compared to untreated control. The onlysignificant decrease in fluorescence of freeze-dried preps occurred fromtime 0 to week 1. No significant changes were noted on storage from week1 through week 4.

[0086] Covalently stabilized phycobilisomes (phycobilisome-antibodyconjugates) suffered substantial degradation immediately followingfreeze-drying in 100 mM M KPi containing 150 mM sodium chloride and0.05% sodium azide. Fluorescence emission at 666 nm decreased by about60%, 666/573 emission ratios decreased five-fold, and absorption spectrawere perturbed. Addition of 1 M sucrose prior to lyophilizationalleviated all signs of degradation. Conjugate freeze-dried insucrose-supplemented KPi over 4 weeks showed no significant change influorescence or absorbance properties compared to liquid controls ortime-zero freeze dried conjugates.

[0087] Derivatization of Phycobilisomes

[0088] Phycobilisomes according to this invention may be modified bycovalent attachment of desired chemical moieties. For use in specificbinding assays, phycobilisomes can be conjugated to ligands, receptors,and/or signal-generating molecules by one-step, two-step, or multi-stepmethods. One-step glutaraldehyde methods proved effective and convenientfor sequential stabilization and conjugation of phycobilisomes withoutintervening purification steps. For achieving conjugation ofphycobilisomes to other molecular species, any conjugation method knownin the art may be used. Direct attachment may be used or secondarystructures such as spacer arms, bridging groups, or carrier moleculesmay be interposed.

[0089] Specific chemical groups can be added to phycobilisomes byquenching the stabilization reactions with suitable substances,including but not limited to cysteine, lysine, glutamic acid,glucosamine, etc. Such chemical groups can be useful for the furthercoupling of distinct molecular species, such as receptors, ligands, orsignal-generating molecules to phycobilisomes. Other examples ofdesirable molecular species include lipids, polysaccharides, orsupramolecular complexes such as multisubunit enzymes or even viruses.Added functional groups can also be used to dimerize or polymerize thephycobilisomes for use as stabilized, isolatable complexes. In aparticularly preferred embodiment, two or more different types ofphycobilisomes can be conjugated to one another to produce aheteroconjugate capable of energy transfer from a donor phycobilisome toan acceptor phycobilisome.

[0090] Attached molecular species may be, but need not be, conjugated tophycobilisomes through added chemical groups. Alternatively, they can bedirectly attached during the stabilization reaction, such as withformaldehyde (FA) or glutaraldehyde (GA). They can also be attached viadifferent spacer arms to alter the spatial or stereochemicalrelationship between the molecular species and the phycobilisome.Carrier molecules, such as bovine serum albumin or even virus particles,may be attached to phycobilisomes and function as a plurality of addedchemical groups for attaching desired chemical moieties to thephycobilisome. Ligands include but are not limited to agonists,antagonists, biotin (or derivatives, such as amido-biotin, imino-biotin,and diamino-biotin), haptens, antigens, carbohydrates, drugs, hormones,transmitters, cofactors, vitamins, toxins, oligonucleotides, nucleicacids, aptamers, and conjugates formed by attaching any of thesemolecules to a second molecule. Receptors include but are not limited toantibodies, antibody fragments, antibody mimetics, molecular mimics andmolecular imprints, molecular recognition units, adhesion molecules,soluble receptors, avidin, streptavidin, lectins, selecting,oligonucleotides, nucleic acids, membrane receptors, cellular receptors,and drug receptors. Signal-generating molecules include, but are notlimited to, phycobiliproteins, dye molecules, colloids, fluorophores andother photoactive molecules, enzymes, ribozymes, molecular mimics,luminescent compounds, oxidizing and reducing compounds and otherelectroactive molecules, photosystem molecules and reaction centers notattached to phycobilisomes in nature such as artificial reaction centersand organizational and coupling molecules used to capture energy inartificial photosynthesis, and even other phycobilisomes.

DERIVATIZATION EXAMPLE 1 Specific Binding Assay Using NoncovalentPhycobilisome-Antibody

[0091] Since unmodified phycobilisomes rapidly dissociate underconditions typically used for preparation and use of specific bindingreagents, noncovalent phycobilisome conjugation required carefulattention to phycobilisome concentration and reaction conditions at eachstep of the process. Murine monoclonal anti-phycoerythrin antibody ofIgG2b subtype (Sigma Chemical Company) was added dropwise with vortexingto P. cruentum phycobilisomes (5.6 mg/ml) in 0.6 M KPi (pH 7.2)containing 2.5 mg/ml BSA to yield molar ratios ranging from 0.5-20IgG2b/phycobilisome. The reaction was allowed to proceed for 30 minutesat room temperature. Immunologic conjugate formation was demonstrated byspecific capture of IgG2b phycobilisome complexes using goat anti-mouseIgG2b antibody immobilized on paramagnetic particles. Fifty microlitersof BIOMAG™ (paramagnetic particles)-goat-antimouse (GAM) IgG2b (30 mg/mlwashed in 0.75 M KPi containing 1% BSA) was added to 40 ul of conjugatemixture containing 200 ug phycobilisomes. After addition of capturereagent, the assay mixture contained phycobilisomes at 2.2 mg/ml with orwithout bound IgG2b in 0.66 M KPi containing 6.7 mg/ml BSA. This mixturewas incubated for 30 minutes at room temperature and separated on amagnetic base (Corning). Absorbance at 545 nm was measured using assaysupernatants diluted 40-fold in 0.75 M KPi. A dose-dependent decrease inabsorbance with increasing IgG2b was observed, indicating specificbinding of the phycobilisome-IgG2b complex by BIOMAG-GAMIgG2b. Maximalspecific binding (26%) occurred at 1-3 ug/test IgG2b, above whichbinding decreased due to insufficient solid phase capacity.

DERIVATIZATION EXAMPLE 2 Preparation of Phycobilisome-Antibody Conjugate

[0092] All steps were performed at room temperature (20-23° C.).Phycobilisomes, isolated from P. cruentum were normalized to aconcentration of 8 mg/ml in 0.75 KPi (pH 7.35) containing sodium azide(2 mM). GA (0.25%) was added dropwise with vortexing over 2 minutes in a10% volume to yield a reaction mixture containing phycobilisomes at 7.27mg/ml and GA at 0.023%. The reaction mixture was left standing for 2hours. Affinity-purified, Fc-specific goat anti-mouse IgG (GAM; OEMConcepts; 2 mg/ml in 10 mM phosphate-buffered isotonic saline containing0.1% sodium azide) was added dropwise with vortexing to yield aGAM/phycobilisome molar ratio of 12:1 (128 ug GAM per mgphycobilisomes). After a 4-hour incubation, the reaction was terminatedby addition of a 10% volume of 1.1 M L-lysine. The quenched reaction wasmixed by rotation for one hour. A 5% volume of freshly prepared sodiumborohydride (Aldrich; 5 mg/ml in 0.1 mM NaOH) was spiked into thereaction mixture with vortexing, followed 5 minutes later by a 10%volume of the same solution. The borohydride-reduced reaction mixturewas stored at 2-8° C. until purification by ultracentrifugation or,preferably, gel chromatography using SEPHACRYL™ (cross-linked co-polymerof allyl dextran and N,N′-methylenebisacrylamide) S300 or SepharoseCL-6B (Pharmacia) equilibrated in 100 mM KPi (pH 7.35) containing 150 mMNaCl and 0.05% NaN₃.

[0093] The conjugates were assessed on the basis of: % recovery (yieldof soluble phycobilisome conjugate as a percentage of phycobilisomestarting material, accounting for procedural losses); absorptivity(AU/mg); fluorescence (concentration-normalized emission intensity; peakratios); and specific binding in a competitive fluoroimmunoassay usingBIOMAG-MIgG as solid phase capture reagent.

[0094] Recovery of soluble material estimated for conjugates purified byultracentrifugation ranged from 72-100%, averaging about 90%. Twelveconjugates prepared from a single lot of phycobilisomes yieldedE₆₆₆/E₅₇₃ ratios of 2.92-3.55 (mean=3.16). Normalized fluorescenceintensity (E₆₆₆ at fixed input) averaged 4.15×10⁶ cps at a conjugateconcentration of 1 ug/ml.

[0095] Up to 60% specific binding of conjugates to BIOMAG-MIgG wasdemonstrated with the solid phase reagent in pseudo-excess (completesaturation was not attempted). Representative binding data are presentedbelow. Fifty microliters of phycobilisome-GAM conjugate (80 ug/ml) wasadded to test tubes containing 50 ul of buffer with or without MIgG plus100 μl BIOMAG-MIgG (1 mg/test). Assay tubes were vortexed and incubatedfor 60 minutes at room temperature. Fluorescence was determined in avolume of 3 ml using 160 ul of assay supernatant withdrawn aftermagnetic separation. Supernatant E₆₆₆ MIgG inhibition MIgG (mass/test)(cps × 10⁻⁵) % bound (cps × 10⁻⁵)  0 22.44 42.1 —  1 ng 27.91 28.0 5.4710 ug 38.77 0.0 16.33

[0096] GA was also used to conjugate GAM antibody to FA-stabilizedphycobilisomes. Phycobilisomes were treated with 2% FA for four hours,quenched with 1 M L-lysine and chromatographed over Sepharose CL-6B.Stabilized phycobilisomes appearing in the void volume were treated withGA and reacted overnight with antibody at a 12:1 molar ratio. Lysinequench, borohydride reduction and purification were performed as per GAconjugation methods (supra). Resultant conjugates exhibited 666/573ratios over 3.0 and 60% specific binding to BIOMAG-MIgG. No significantdecrease in fluorescence intensity (E₆₆₆) or immunoreactivity (%binding) was detected with overnight room temperature storage at aworking concentration in 10 mM KPi-based assay buffer or with storagefor one week in 100 mM KPi-based assay buffer.

[0097] Site- or Regio-Specific Derivatization

[0098] Attachment of a molecular species to a phycobilisome may besite-specific or regio-specific, for example, by derivatizing aparticular portion of a phycobilisome to orient the light collectionproperties of this invention. Site-specific or regio-specific attachmentmeans preparation of a conjugate comprising a phycobilisome and a secondstructure (e.g., a second molecular species, a new chemical group orplurality of new chemical groups, or a solid support), wherein thesecond structure is attached to the phycobilisome at chemically,functionally or topologically defined site(s). Site-specifc attachmentinvolves attachment to a particular chemical moiety, such as a reactivegroup or a site that specifically binds an affinity reactant, while forregio-specific attachment, the focus is on toplogical position of theattached species rather than on the particular chemical site. However,the art recognizes some overlap between these terms.

[0099] Site-specific attachment may be covalent or non-covalent.Preferred attachment site(s) vary depending on the application and thecomposition of the phycobilisomes to be used. For a single rod,preferred sites include the cap polypeptide (i.e., “cap protein”),sensitizing biliproteins making up the outermost discs, the terminalacceptor, and the rod or rod-core linker polypeptide(s). For a rod-coresubassembly, preferred sites include cap proteins, sensitizingbiliproteins of the rod(s) and the terminal acceptor and linkerpolypeptide(s) of the core. For phycobilisomes further comprising ananchor polypeptide and/or reaction center and/or photosystem, specificpolypeptides or proteins or peptide sequences or amino acid residues canserve as targets for site-directed attachment. In each case, wild-typeproteins and peptides can be replaced by mutant, recombinant orchemically modified sequences or residues to introduce distinct reactivegroups in topologically or functionally preferred sites. For example,one or more phycobilisome proteins can be glycosylated (e.g., byperiodate or hydrazide chemistry) and the saccharide residuesspecifically bound by lectin-conjugates of molecular species, such assignal-generating molecules.

[0100] Site-specific or regio-specific attachment of a molecular speciesto a phycobilisome may be achieved inter alia by means of monovalent orpolyvalent receptors, such as antibodies or other peptides, which arespecific for one of the component proteins of the phycobilisome. Apolyvalent receptor contains two or more binding sites for its ligands.The polyvalent receptors utilized in the present invention may bepolyspecific, i.e., they may contain binding sites for two or moredistinct ligands. Thus, the polyspecific receptors can be used to link aphycobilisome to another species of molecule. Alternatively,site-specific attachment to phycobilisomes by non-coralent means can beachieved using peptides or other heteropolymers selected bycombinatorial methods (see, e.g., Fodor, et al., 1991, Science,251:767-772; Kauffman, S. (1994), “Random chemistry,” Ber. Bunsenges.Phys. Chem., 98:1142-1147; Kenan, D. J., et al. (1994), “Exploringmolecular diversity with combinatorial shape libraries,” Trends inBiological Sciences (TIBS), 19:57-64; Ostresh, J. M. et al. (1994)“Libraries from libraries: Chemical transformation of combinatoriallibraries to extend the range and repertoire of chemical diversity,”Proc. Natl. Acad. Sci. USA, 91:11138-11142; Hart, S., 1993, “Test-tubesurvival of the molecularly fit,” BioScience, 43:738-741).Phycobilisomes can also be covalently attached to receptors or ligandsby numerous methods well-known in the art of protein conjugation (cf.Tijssen¹, Wong² and Pierce³ and references therein, included herein byreference), and the attachment may include the use of intervening spacerarms, bridging groups, carrier molecules, and the like.

[0101] Site-specific attachment may also be achieved throughmonospecific and monovalent ligands or receptors. For example, anantibody specific for a particular site on the phycobilisome can bereduced to yield two half-antibody molecules containing free sulfhydrylgroups. The reduced product can then be specifically bound to thephycobilisome to provide a unique conjugation site for asulfhydryl-reactive conjugation reagent. Alternatively, thehalf-antibody molecules can be conjugated either through the freesulfhydryl groups or amines or carboxyls or the carbohydrate chains ofthe C_(H)2 domain to a second molecule, e.g., a different ligand orreceptor or signal-generating molecule. The conjugate can then bespecifically bound to the targeted site on the phycobilisome. The sametechnique can be used to target Fab fragments or conjugated Fabfragments to phycobilisomes by first preparing enzymatic digests of anantibody against a phycobilisome constituent. F(ab′)₂ fragments preparedin this way can be reduced to yield monovalent Fab′ fragments with freesulfhydryl groups. Because these monospecific, monovalent fragments aresignificantly smaller than intact antibody molecules, they are preferredfor certain applications that require functional coupling betweenphycobilisomes and attached signal-generating molecules. For example,anti-allophycocyanin (anti-APC) Fab′ fragment can be conjugated to aligand such as a hapten (e.g., a drug, hormone, pesticide or otheranalyte) or a DNA probe (e.g., for detection of a target nucleic acidsequence) so that the conjugated phycobilisome can serve as a label forspecific binding reactions localized to a particular region of thephycobilisome. In this mode of operation, the phycobilisome conjugatefunctions as a directional light-harvesting antenna coupled to aspecific binding reaction.

[0102] Using an antibody directed against a phycobilisome constituentfor regio-specific recognition, attachment can also be directed to thecarbohydrate groups of the C_(H)2 domain of the Fc region, e.g., byperiodate oxidation of the polysaccharide sugar residues to generatealdehydes followed by modification or crosslinking with a hydrazidereagent (e.g., Wong (1991), Pierce (1994)).

[0103] Alternatively, noncovalent attachment of a ligand, receptor orsignal-generating molecule to carbohydrates in the Fc region of ananti-phycobiliprotein or anti-linker polypeptide antibody can beachieved using an affinity reagent, e.g., a lectin or selectin withsuitable sugar specificity. Additional techniques for site-directedattachment include, without limitation, genetic methods, preparativemodifications, interfacial methods, reconstitution of phycobilisomeswith genetically or chemically modified or immobilized constituents andself-assembly of conjugates comprising selected molecules non-covalentlyattached to phycobilisomes. Genetic methods include, for example, use ofsite-directed mutagenesis, recombinant techniques and fusion proteins toincorporate a unique attachment site (e.g., a poly-his region or surfacecysteine residue or amino acid analog) in a particular linkerpolypeptide or protein, and use of applied molecular evolution to screenand select linker polypeptide and phycobiliprotein variants for desiredrecognition properties or attachment sites.

[0104] Regio-specific modification or conjugation can also be directedto functional groups on or near the biliprotein chromophores or theirapoprotein attachment sites. The tetrapyrrole groups of phycocyanobilin,phycobiliviolin, phycoerythrobilin and phycourobilin and the thioetherlinkages between the chromophores and the apoproteins comprisefunctional groups not represented on the phycobilisome surface. Thesegroups provide targets for genetic and chemical modification, and suchmodification can and typically does alter the spectral properties of themodified products relative to unmodified phycobilisomes. For certainapplications (e.g., use of phycobilisomes as sensitive labels forhomogeneous specific binding assays), it is preferable toregio-specifically modify phycobilisomes without perturbing absorptionand fluorescence properties. For other applications (e.g., use of two ormore phycobilisome labels in multicolor flow cytometry or multiplexedsensors), it is preferable to co-select among multifactoral combinationsof modification reagents (e.g., number and type of reactive groups,length of spacer arm(s)) and reaction conditions (e.g., reagentconcentrations, reaction time, temperature, pH, solvent and bufferconditions) and phycobilisome preparations (e.g., source, isolationprocedure, stabilization protocol) those modified products that exhibitthe most desirable spectral properties. In a particularly preferredembodiment, phycobilisomes modified near biliprotein chromophores arereconstituted from isolated linker polypeptides and phycobiliproteinswhich have been site-specifically modified by chemical, affinity-basedor genetic methods disclosed elsewhere in this specification.

[0105] Regio-specific modification of phycobilisomes according to thisinvention includes stabilization of phycobilisomes in situ (e.g.,Clement Metral et al. (1971)) so that peripheral rods are exposed to thesolution phase, but thylakoid membrane-embedded constituents areinaccessible to water-soluble conjugation reagents. The peripheral rodside of the phycobilisome can then be selectively modified withoutaltering constituents embedded in the membrane. Phycobilisomemodification conditions can then be adapted to either encourage ordiscourage reagent access to sterically or kinetically hindered sitesnear the core-membrane interface. Alternatively, functional groups ofthe peripheral rods (e.g., amine or carboxyl groups) can be selectivelyblocked. Stabilized, partially blocked phycobilisomes can then beisolated from thylakoid membranes, leaving membrane-protected sites ofthe core side available for conjugation. A similar method can bedeveloped using affinity reagents with bulky substituents to stericallyocclude targeted regions of the phycobilisome (e.g., the terminalacceptor or APC core) followed by rapid modification of the mostaccessible sites, e.g., using a photoactivatable crosslinker with pulsedillumination, a photo-affinity reagent, an immunoaffinity conjugate, orthe like. Alternatively, regio-specific binding to a phycobilisome maybe accomplished using a reagent that specifically recognizes sitesdistributed over the entire surface by covalently blocking a portion ofthe specific sites on the phycobilisome and then non-covalently bindingthe reagent to the unblocked sites.

[0106] Interfacial methods rely on the structural orientation ofphycobilisomes or the relative solubility of phycobilisomes and a secondmolecular species exposed to a two-phase system, e.g., a polar-nonpolarsolvent mixture or solid-liquid interface. Aqueous-nonpolar two-phasesolvent systems can be selected to partition the hydrophilic,biliprotein-rich side of the phycobilisome to the aqueous phase whilefavoring association of the hydrophobic anchor polypeptide with thenonpolar phase. Alternatively, a particular region of the phycobilisomecan be rendered especially hydrophobic using an affinity reagentconjugated to a hydrophobic or lipophilic substituent (e.g., a lipid orcolloid or polymer). Similar effects may be achieved by regio-specificderivatization of phycobilisomes with either hydrophilic moieties orlipophilic moieties using derivatization techniques described above.Phycobilisomes can also be oriented electrophoretically (e.g., Gaglianoet al. (1985)) followed by regional modification through transientexposure of one side of the gel to a selected protein modificationreagent. Similar methods can be developed using affinity supports toorient the phycobilisome on a matrix and to preferentially occludeparticular region(s) of the phycobilisome, e.g., the anchor polypeptideor terminal acceptor. Solid-liquid phase systems provide preferentialaccess of conjugation reagents to the solution phase side of thephycobilisome and impaired access to the solid phase side.Phycobilisomes can be oriented on a solid phase by self-assembly usinghydrophobic or amphipathic membranes, films, polymers or coatings.Alternatively, the desired orientation can be achieved usingaffinity-based methods, e.g., by specific binding to an immobilizedanti-APC, anti-linker polypeptide, or anti-anchor polypeptide antibody.

[0107] Phycobilisomes may also be immobilized to a manufactured solidsupport, such as a microtiter dish, microparticle, polymeric bead,polymer matrix, polymer, synthetic membrane, liposome, glass, etc. Suchimmobilization does not include the attachment of phycobilisomes to thethylakoid membrane as occurs physiologically, via specific receptors inthe thylakoid membrane. The phycobilisomes may first be isolated fromalgal cells and then attached to the solid support, or they may bemodified, conjugated, or stabilized, prior to attachment. The attachmentmay be covalent or noncovalent, specific or nonspecific. The method ofattachment may be optimized to achieve a preferred orientation of thephycobilisomes relative to the solid surface. In one embodiment,phycobilisomes derivatized with lipophilic moieties, such as fatty acidsor fatty acid analogs, may be immobilized by hydrophobic partitioning oflipophilic moieties into a lipid bilayer membrane. Optionally, the lipidbilayer membrane may itself be immobilized on a solid support.Alternatively, a single type of constituent phycobilisome protein,either linker polypeptide, anchor protein or phycobiliprotein, may beused as the attaching moiety to a solid support. For some applications,it may be desirable that the phycobilisomes be attached in an orderedarray, such as in a grid or other pattern.

[0108] Self-Assembly of Phycobilisomes

[0109] Phycobilisomes, isolated as described herein, are capable ofself-assembly after gentle dissociation. After gentle dissociation inlow ionic strength buffers, native phycobilisomes will spontaneouslyself-assemble when the buffer concentration is increased, e.g., to 0.75M phosphate. Reassociation is driven by one or more specific linkerpolypeptides that recognize the constituent phycobiliproteins andarrange them into a very efficient energy transduction system in anon-covalent manner. Self-assembly is a powerful tool that enablesproduction of novel and useful compositions, e.g., stabilized andconjugated and immobilized hybrid or chimeric phycobilisomes, andmethods, e.g., attachment and functional coupling of phycobilisomes andchimeric phycobilisomes to transducers by self-assembly (which may befollowed by stabilization and/or conjugation).

[0110] There is a broad literature on the dissociation and reassociationof phycobilisomes (e.g., Canaani et al. (1980) FEBS Letters,115:225-229; Lipschultz and Gantt (1981) Biochemistry, 20:3371-3376;Cananni and Gantt (1982) Proc. Nat. Acad. Sci. USA, 79:5277-5281; Glickand Zilinskas (1982) Plant Physiol., 69:991-997; Zilinskas and Howell(1983) Plant Physiol., 71:379-387; Isono and Katoh (1983) Plant Cell.Physiol. 24:357; Cananni and Gantt (1983) Biochim. Biophys. Acta,723:340). This self-assembly of the phycobilisome can be used to createchimeras using components from different phycobilisomes (from differentorganisms). Any such chimera (or hybrid) may have properties (e.g.,absorbance or fluorescence emission, quantum yield) which differ fromthe parent phycobilsomes in a manner useful for detection and signaltransduction. In addition, the self-assembly can be used in assays basedon proper assembly of the complex (e.g., phycoerythrin/phycocyanin rodassociation via a specific binding reaction to the allophycocyanin coreyielding emission at 666 nm).

[0111] An example of how self-assembly works is described here.Phycobilisomes may be dissociated at defined concentrations of phosphatebuffer such that peripheral phycobiliproteins are dissociated first(Nies and Wehrmeyer (1981) Arch. Microbiol., 129:374-379). This approachhas been described previously for a number of organisms (Gantt etal.(1979) Plant Physiol., 63:615-620; Cananni et al. (1980) FEBSLetters, 115:225-229); optimization for phycobilisomes from otherorganisms can be accomplished by placing them in a phosphateconcentration that differentially destabilizes the phycobilisomes andthen dialyzing. After about 3 hours the material is centrifuged topellet the phycobilisomes, while dissociated phycobiliproteins remain inthe supernatant. This can be done in a sequential manner to release thephycoerythrins, phycocyanins and allophycocyanin in a stepwise fashion.These components can then be reassociated by putting the fractionstogether at a phosphate concentration (e.g., 0.75 M) that favorsreassociation. For in vitro association, fractions may be mixed at 0.75M potassium phosphate (pH 7.0) containing 2 M sucrose and incubated for3 h. Samples of this reassociation mixture can then be put over adiscontinuous sucrose gradient and centrifuged to equilibrium. Intact,functionally active phycobilisomes may be isolated in the 1-2 M sucrosefraction. Hybrid phycobilisomes can be prepared by this method, so longas the linker polypeptides are compatible (e.g., by mixing theallophycocyanin fraction from Fremyella with thephycocyanin/phycoerythrin fraction from Nostoc, Canaani and Gantt (1982)Proc. Nat. Acad. Sci. USA, 79:5277-5281).

[0112] Where the intention is to specifically label the phycobilisome atthe core (allophycocyanin) or terminal emitter region, theallophycocyanin fraction can be isolated and biotinylated usingNHS-biotin (PIERCE CHEMICAL COMPANY). Once biotinylated, theallophycocyanin fraction may be added back to thephycocyanin/phycoerythrin fraction and allowed to reassociate. Thereassociated phycobilisome now has biotin on the terminal emitter suchthat streptavidin chemistry can be used to specifically label theterminal emitter, to attach the phycobilisome through the terminalemitter for functional coupling, or to add additional reactive groups.

[0113] Phycobilisomes and hybrid structures can also be oriented in asite-directed manner on a solid support by reconstitution from partiallydissociated phycobilisomes or isolated phycobiliproteins and linkerpolypeptides in the presence of an immobilized phycobilisomeconstituent, e.g., a linker polypeptide, anchor polypeptide or reactioncenter. The immobilized phycobilisome constituent can be directlyattached to a solid support, or it can be specifically bound to animmobilized ligand or receptor or attached through a membrane or film orpolymer or coating.

[0114] Self-assembly of phycobilisomes having exogenous hydrophobicmolecules complexed to the anchor polypeptide can also be achieved. Thebiliprotein molecules of the phycobilisome are acidic and hydrophilic.The linker polypeptides, by contrast, are basic and very hydrophobic(Glazer, A. N. 1984, “Phycobilisomes: a macromolecular complex optimizedfor light energy transfer,” Biochim. Biophys. Acta, 768:125-157; Glazer,AN., 1985a, “Light harvesting by phycobilisomes,” Annual Rev. Biophys.and Biophys. Chem., 14:47-77). There is therefore a tendency for added,water-insoluble molecules to associate with the exposed anchorpolypeptide region by hydrophobic interactions. Methods can be developedto attach hydrophobic molecules, complexes or groups of molecules to theanchor polypeptide region by selecting the solvent system, molar ratio,assembly conditions and purification methods appropriate to the selectedmolecule. Alternatively, hydrophilic molecules or complexes can first beconjugated to a hydrophobic carrier and then attached by hydrophobicinteractions to the anchor polypeptide region. Molecules or conjugatesattached to specific phycobilisome regions in this manner can then becovalently attached by crosslinking methods well-known in the art. In apreferred embodiment, phycobilisomes or subassemblies are modified withhydrophobic, lipophilic or amphipathic substituents and incorporated orreconstituted in hydrophobic or amphipathic matrices by self-assembly,e.g., within a liposome, monolayer, film, membrane or membrane mimetic.Suitable hydrophobic and amphipathic matrices are well-known in the art(e.g., U.S. Pat. Nos. 3,966,580 (1976) and 4,490,216 (1984); Betageri,et al. (1993), Liposome Drug Delivery Systems, Technomic PublishingCompany, Lancaster, Pa.; Gregoriadis, G. (Ed.) (1993), LiposomeTechnology, Volumes 1, 2 and 3, Boca Raton, Fla., CRC Press; Guo, et al.(1990), “Novel anti-fungal drug delivery: stable amphotericinB-cholesterol sulfate disks,” Int. J. Pharm., 75:45-54; Fendler, J. H.(1982) Membrane Mimetic Chemistry, Wiley-Interscience, N.Y; Janoff, etal. (1988), “Unusual lipid structures selectively reduce the toxicity ofamphotericin B,” Proc. Natl. Acad. Sci. USA, 85:6122-6126; Machy, et al.(1987), Liposomes in Cell Biology and Pharmacology, John LibbeyEurotext, London).

[0115] Phycobilisome preparations comprising reaction centers andphotosynthetic constituents can also be prepared and modified to providestabilized phycobilisomes, phycobilisome complexes or conjugates orimmobilized reagents of the instant invention (Clement-Metral andLefort-Tran (1971) FEBS Letters, 12:225-228; Gantt et al. (1988) Meth.Enzymology, 167:286-290). A phycobilisome-photosystem II complex hasbeen isolated (Gantt et al. (1988) Meth. Enzymology, 167:286-290). Thecells were rinsed in distilled water then suspended using a glasshomogenizer in a buffer (0.5 M sucrose, 0.5 M potassium phosphate (pH7.0), 0.3 M potassium citrate, 15 mM MgCl₂) at 4° C. The cells werebroken in a French pressure cell. To this lysate, 0.12% (v/v)lauryldimethylamine oxide (LDAO) detergent was added to give a detergentto chlorophyll ratio of 3.5-4.1:1 (w/w). This mixture was incubated for30 min in the dark with gentle stirring. The extracted lysate wascentrifuged at 27,000×g for 30 min. The clarified lysate was placed on adiscontinuous sucrose gradient and centrifuged at 130,000×g for 11 h.The phycobilisome-PSII complex was collected between the 1 M and 2 Msucrose layers. This was diluted to twice the volume with the originalbuffer and centrifuged at 27,000×g for 30 min. The supernatant containedthe phycobilisome-PSII complex which can be used as is or can beconcentrated by ultracentrifugation at 270,000×g for 3 h. Thispreparation method can be used for red algae and, with modification, forcyanobacteria.

[0116] Preparations comprising phycobilisomes bound to thylakoidmembranes (e.g., Clement-Metral and Lefort-Tran (1971) FEBS Letters,12:225-228; Katoh and Gantt (1979) Biochim. Biophys. Acta, 546:383-393;Laczkó and Kaiseva (1987) Photochem. Photobiol., 46:421-425 can also beused to produce stabilized or conjugated or immobilized phycobilisomesor phycobilisome complexes of the instant invention. In one method(Clement-Metral and Lefort-Tran (1971) FEBS Letters, 12:225-228), wholealgal cells were treated with 2% w/v glutaraldehyde for 15 min at 4° C.These cells were then washed twice in 0.02 M phosphate buffer (pH 6.9)by centrifugation. This procedure can be modified by methods of theinstant invention to include quench and/or reduction steps prior tocentrifugation to obviate excessive cell and membrane cross-linking.Quenching may be achieved by addition of excess amines (e.g.,polylysine, lysine, glycylglycine, glutamine), and reduction may beachieved using borohydride, cyanoborohydride, dithiothreitol and thelike. The washed cells are then disrupted by French pressure celltreatment and the lysate centrifuged 30 min at 12,000×g. The clarifiedsupernatant is put on a 3-48% linear sucrose gradient and centrifugedfor 5 h at 22,500 rpm on a Spinco SW25.1. A heavily pigmented layer inthe middle of the gradient contains stabilized phycobilisomes attachedto membrane fragments.

[0117] Use of Modified Phycobilisomes

[0118] Phycobilisomes as Detectable Labels

[0119] The phycobilisomes of the present invention are particularlywell-suited for use in specific binding assays. These may beimmunological assays, immunohistochemistry, cytometry, cell sorting,ligand- or receptor-binding assays, protein-protein binding assays,protein-nucleic acid binding assays, and even nucleic acid-nucleic acidbinding assays (e.g., hybridization). The phycobilisomes are typicallyused to label one of the specific binding partners involved in theassay. For example, the phycobilisomes may be used to label a ligand orreceptor that specifically binds to the analyte to be assayed.Alternatively, the phycobilisomes may be used to label a reagentmolecule which is a ligand or receptor that competes with the analytefor specific binding to its specific binding partner. Labeling may bedirect, where the phycobilisomes are attached to a first ligand orreceptor that specifically binds to or competes with the analyte.Alternatively, labeling may be indirect, where the phycobilisomes areattached to a second ligand or receptor that specifically binds to afirst ligand or receptor. The attachment of phycobilisomes to a specificbinding partner may be covalent or noncovalent and may be accomplishedusing intervening chemical groups such as spacer arms, bridging groups,carrier molecules, molecular complexes, and the like. The phycobilisomesmay also be part of a signal-generating system in which otherfluorophores emit light upon transfer of directional energy to or fromphycobilisomes. The phycobilisome may be stabilized prior to itsattachment to the specific binding partner or may be directly conjugatedthereto. Alternative means of preparation of phycobilisomes includefreezing, freeze-drying, and other methods of dehydration. It isdesirable that freezing of phycobilisomes be done in the presence ofsucrose, in concentrations from 0.1 to 1 M. Other stabilizing agentssuch as sugars, salts, polymers, and cosolvents may be used.Particularly useful agents include trehalose, sorbitol, and dextran.

[0120] Soluble, stabilized phycobilisomes of the present invention havea number of uses that do not require conjugation to specific bindingpartners. For example, they can be used as sensitive tracers fordilution and perfusion studies and as molecular size markers foranalytical techniques. In a preferred embodiment, they can be used todetect potentially hazardous spills. Phycobilisomes can be mixed with apotentially hazardous substance prior to its use to yield a finalconcentration of phycobilisomes of less than about ten parts permillion. The phycobilisomes can then be detected in the event that thehazardous substance is accidentally spilled or removed from its properlocation. The presence of the detectable phycobilisomes indicates that aspill has occurred. Alternatively, a first surface, substance or itemcan be treated with a coating or solution of phycobilisomes (andoptionally allowed to dry), so that the appearance of detectablephycobilisomes on a second surface, substance or item indiates that atransfer of material has occurred, potentially including hazardous orotherwise undesireable contamination.

[0121] Specific binding assays according to the present invention may bequalitative or quantitative. Small molecules (involving a single bindingsite) or large molecules (involving more than one binding site) may beused as analytes. Analytes which may be measured or detected usingspecific binding assays according to the present invention includedrugs, ligands, antigens, antibodies, carbohydrates, hormones, and thelike. Detection means for determining the results of the binding assaymay be by visual inspection, photometry, fluorometry, laser, orelectrochemical means.

[0122] Any assay format known in the art may be utilized, includingwithout limitation, homogeneous assays, heterogeneous assays,competitive assays, and sandwich assays. In homogeneous assays, specificbinding between two binding partners (i.e., ligand and receptor)influences activity of a detectable label; no separation of bound andunbound reagents is required. In heterogeneous assays, separation ofbound and free reagents is required to determine the amount of bindingwhich has occurred. Quantification of such assays can be accomplished byeither photometric, fluorometric or optoelectronic means. Alternatively,qualitative results can be obtained by visual inspection. Because nativephycobilisomes spontaneously dissociate under routine conjugation andassay conditions, they must be stabilized prior to use in mostconventional assay formats. However, in some instances it will bedesirable to use the dissociation of phycobilisomes to amplify thesignal generated. Thus, after using phycobilisomes in an assay and priorto detection, dissociation may be induced in order to take advantage ofthe individual fluorescent properties of the constituentphycobiliproteins.

[0123] Another means of using phycobilisomes to amplify a specificbinding assay-signal is to use two or more labeled species specificallybound to one another, where at least one label is a phycobilisome. Thisapproach is analogous to the well-known assay technique of using alabeled secondary antibody to amplify a primary immunological bindingreaction. For phycobilisome-based signal amplification, it is preferredthat both a primary and secondary specific binding reagent be labeled.For example, a secondary phycobilisome-labeled species (e.g., aphycobilisome-streptavidin conjugate) may be bound to a primaryphycobilisome-labeled species (e.g., a biotinylatedphycobilisome-antibody conjugate) via a secondary ligand-receptor pair(in this case, biotin-streptavidin). The use of secondary labeling iswell-known in the art, as exemplified by such commonly usedligand-receptor pairs as avidin and biotin, fluorescein andanti-fluorescein, peroxidase and anti-peroxidase, digoxigenin andanti-digoxigenin, antibody and anti-antibody, or oligonucleotide probeand target. Thus, any ligand-receptor pair, such as biotin and avidin,can act as a bridge, linking primary and secondary labels.Phycobilisome-based amplification can be achieved in this manner usingphycobilisomes as either primary label, secondary label, or both.Phycobilisomes are particularly advantageous as the primary label foramplification of this sort, because phycobilisomes can serve asparticularly large scaffolds to hold a large number of secondary labels.It will be apparent to one skilled in the art that complexes of primaryand secondary or even additional labels may be preformed prior to addingthe label species to the assay. The primary and secondary or otherlabels may be phycobilisomes with different spectral properties.

[0124] In heterogeneous specific binding assays, a reaction mixture isformed by contacting a liquid medium with a labeled conjugate comprisinga phycobilisome attached to a specific binding partner. A bound phaseand a free phase of said labeled conjugate are formed. The relativeproportion of labeled conjugate in the two phases is a function of thepresence and amount of analyte in the liquid medium. The bound phase andfree phase are then separated. The analyte in the liquid medium isdetermined by detecting or measuring phycobilisomes in the bound phaseor in the free phase.

[0125] Particularly useful heterogeneous assays employ a solid phase, towhich either the analyte or an analyte analog or a specific bindingpartner is attached. The solid phase facilitates the separation of boundlabeled species from free labeled species in a heterogeneous specificbinding assay. Popular solid phase reactions include Southern, Northern,and Western blotting assays. Any suitable solid phase can be used,chosen for its acceptability in a particular assay environment. Theseinclude synthetic membranes, polymers, microparticles, and glass.

[0126] A homogeneous specific binding assay method can also be readilyperformed. In a preferred method, a phycobilisome-labeled ligand orreceptor is used in conjunction with a second fluorophore-labeledspecific binding partner. Directional energy transfer withinphycobilisomes enables their use as particularly efficient photon donorsor acceptors in such fluorescence energy transfer assays, although suchinternal energy transfer is not absolutely required. For example, ananti-allophycocyanin (anti-APC) Fab′ fragment labeled to high specificactivity with a near infrared cyanine dye such as CY5.5 (Amersham LifeScience, Arlington Heights, Ill.) can be used to attach and functionallycouple the dye to a rhodophytic or cyanobacterial phycobilisome whichhas peripheral rods attached to a phycocyanin/allophycocyanin core.Excitation of the phycobilisome anywhere within its broad absorptionspectrum then results in efficient energy transfer to the CY5.5 dye, asevidenced by an emission peak around 692 nm, representing an infraredshift of about 30 nm compared to the unmodified phycobilisome.

[0127] In a particularly preferred embodiment, an antibody or Fabfragment or other receptor or ligand specific for a phycobilisomeconstituent can first be specifically bound to a selected site on thephycobilisome and then covalently crosslinked in place using, e.g., FAor GA or other homobifunctional or heterobifunctional crosslinkingagents well-known in the art (e.g., Tijssen (1985), Wong (1991) andreferences therein) which are available with or without variable lengthspacer arms (e.g., Pierce Catalog & Handbook (1994)). In anotherpreferred mode of operation, an anti-APC or anti-anchor polypeptide Fabfragment can be labeled with both a signal-generating molecule (e.g., anacceptor fluorophor such as CY5.5) and a specific binding partner (e.g.,a hapten or DNA probe). In this type of embodiment, specific binding ofan anti-hapten antibody or nucleic acid target to the noncovalent,functionally coupled phycobilisome-conjugate complex can dissociate thecomplex, resulting in an analyte-specific signal (e.g., the spectralshift resulting from the uncoupling of energy transfer as theCY5.5-labeled Fab fragment dissociates from the phycobilisome). Thistype of reagent complex can be used for homogeneous specific bindingassays, as specific binding directly influences the energy transferactivity of the phycobilisome-acceptor complex without the need forphysical separation and wash steps.

[0128] Energy Transfer via Phycobilsomes

[0129] A number of earlier methods and compositions rely on highmolecular weight complexes, polymers, particles and colloids to producehighly detectable labels. Urdea et al. (U.S. Pat. No. 5,124,246), forexample, disclose linear or branched oligonucleotide multimers useful asamplifiers in biochemical assays. DNA dendrimers that provide a genericmethod for signal amplification are described in U.S. Pat. Nos.,5,175,270; 5,484,904; and 5,487,973. High molecular weight fluorescentproteins and dextrans are also known in the art, as are synthetic dyepolymers (e.g., U.S. Pat. No. 5,019,521). High intensity fluorescentmicrospheres comprising multiple energy transferring dyes with suitablespectral overlap to yield single a emission peak at a selectedwavelength are described in U.S. Pat. No. 5,326,692.

[0130] The phycobilisomes, stabilized phycobilisomes, modifiedphycobilisomes and phycobilisome complexes disclosed herein provide animportant, distinct and useful property that is absent in above-citedart. Phycobilisomes function in nature as antenna structures thatefficiently harvest light. The light-harvesting properties ofphycobilisomes depend on an intrinsic structural and functional“sidedness,” meaning that photons are collected from one “side” (i.e.,peripheral rod(s)) and re-emitted from a second “side” (i.e., theterminal acceptor). Directional energy transfer can be demonstrated inphycobilisomes comprising a single rod (e.g., Zilinskas, et al. (1986),“Phycobilisome structure and function,” Photosynthesis Research,10:7-35) and even within rod subelements comprising hexameric doublediscs (Glazer (1984)). Unlike prior art labels such as fluorescentmicrospheres and DNA dendrimers, phycobilisomes can therefore performfunctions that rely on directional transduction of energy from incidentphotons to a fluorescent or optoelectronic signal or to a chemical orelectrochemical reaction, particularly to perform useful work.

[0131] Phycobilisomes of the instant invention can be functionallycoupled, preferably by site-directed attachment, to a signal-generatingmolecule or to a transducer. For example, phycobilisomes can be coupledto a signal-generating molecule such as a second fluorophor (e.g., adonor or acceptor), a light-driven or bioluminescent enzyme (e.g., anATPase or luciferase) or an artificial reaction center (i.e., a moleculecapable of photoinduced charge separation). Alternatively oradditionally, they can be attached to an optoelectronic transducer(e.g., photovoltaic cell) so that one region of the phycobilisome (e.g.,the terminal acceptor or reaction center) is in direct evanescent orphotoelectric communication with the device. The light-harvestingfunction of phycobilisomes can thus be coupled to an optoelectronictransducer much like a radio antenna is connected to a receiver.

[0132] Site-directed attachment of a signal-generating molecule to aparticular site on the phycobilisome (e.g., peripheral rod, terminalacceptor, anchor polypeptide, reaction center, or photosystem complex)provides a way to capture. harvested light energy through coupling toother molecular processes (e.g., catalysis, signal transduction,artificial photosynthesis). In other words, molecules or conjugatescapable of interacting with particular regions of the phycobilisome(e.g., peripheral rods, core phycobiliproteins, a specific linker oranchor polypeptide or topological site, or a designer group or peptidesequence) can be attached to the desired site in such manner that theresulting phycobilisome conjugate can perform useful functions,particularly functions that depend on the sidedness of the antenna. Forexample, attachment of a specific recognition site at the terminalacceptor region can provide a target, catalytic site or distinctfunctional group through which secondary molecules may be attached in asite-specific manner. The antenna function of the phycobilisome can thenbe modulated or supplemented by the activity of attached molecules,which may be ligands, receptors, signal-generating molecules or simplychemical groups, molecules or complexes foreign to the surface ofphycobilisomes as they are found in nature. In addition, thephycobilisome moiety or attached molecules of such conjugates can beused to report interactions (e.g., catalysis, specific binding) betweenattached molecules and a particular sample or environment.

[0133] Immobilization of phycobilisomes to a solid support may be bymeans of a covalent or non-covalent linkage. Non-covalent methodsinclude, e.g., passive adsorption, affinity-based methods,encapsulation, entrapment and controlled deposition. Immobilization mayyield a structurally ordered product. The phycobilisomes may be orientedin a particular manner with respect to the solid support (e.g., “coreup” or “core down”). Alternatively the spacing between phycobilisomes onthe solid support may be defined or patterned, for example, to form atwo-dimensional array or grid.

[0134] Methods for physically and chemically patterning surfaces (e.g.,by lithography, etching, plasma deposition, plating, bonding andtemplating techniques) and for preparing biomolecular arrays on surfaces(e.g., by in situ synthesis, robotic dotting and spotting, lithographicmethods such as photolithography, piezoelectric and inkjet technologies)are known in the art (e.g., Drmanac, et al. (1989), “Sequencing ofmegabase plus DNA by hybridization.” Genomics 4:114-128, Fodor et al.(1991), Pirrung et al. (1994), Crkvenjakov, et al. (1994), “Sequencingby hybridization: Toward large-scale compilation of human cDNAsignatures.” Human Genome Program, U.S. Department of Energy,Contractor-Grantee Workshop III, February 7-10 (1993), p. 77, HumanGenome News (1994), “Workshop on sequencing by hybrization.” HumanGenome News 5(5):12-13). Arrays, grids or other patterns of a singlephycobilisome or conjugate preparation or of multiple differentphycobilisome or conjugate preparations can be achieved either bydeposition of phycobilisome complexes, phycobilisomes, subassemblies,isolated proteins, peptides, linker polypeptides, anchor polypeptides,ligands or receptors or by in situ synthesis of peptides, polypeptidelinkers, nucleic acid molecules or other affinity reagents on solidsupports. Attachment surfaces may be modified by any of a wide varietyof techniques well-known in the art, such as addition of amino groups byfuming of nitrous acid, bromoacetylation, oxidation by use of plasma,ultraviolet light or an electron beam as energy source in the presenceof oxygen and air, chemical grafting, coating with bifunctional reagents(e.g., GA) or polymers (e.g., latex), covalent attachment of linker orspacer molecules, and noncovalent attachment of affinity spacers (e.g.,to aromatic groups).

[0135] A particularly preferred embodiment of the instant invention is aphycobilisome-based biotransducer comprising a phycobilisome orphycobilisome conjugate functionally coupled to a transducer. Typically,the phycobilisome of a phycobilisome-based biotransducer is operativelyassociated with, attached to, immobilized at, packaged with, orotherwise structurally or functionally inseparable from the transducer.A phycobilisome-based biotransducer can also be a two-component (ormulti-component) product or system comprising a transducer component anda disposable, replaceable, reusable or upgradeablephycobilisome-containing cartridge, module, slide, disk, film, layer,fiber, connector, attachment or part that serves as an interface betweenthe phycobilisome and the transducer. In this case, thephycobilisome-containing component is physically separable from thetransducer component but must be inserted, attached, rejoined orreplaced to form the functionally coupled two-component system capableof performing the intended function. The functionally coupled transducerconverts an activity, energy or property of the biological or biomimeticmolecule(s) (e.g., the phycobilisome(s) or phycobilisome conjugate(s))to useful work or information or a detectable signal. Transducers of theinstant invention may be electronic, electrical, optical,optoelectronic, electromechanical, electrochemical, photochemical,thermal or acoustical devices and include, without limitation, opticalfibers and waveguides, evanescent waveguides, light-addressablepotentiometric devices, photovoltaic devices, photoelectric andphotochemical and photoelectrochemical cells, conducting andsemiconducting substrates, molecular and nanoscale wires, gates andswitches, charge-coupled devices, photodiodes, electrical andoptoelectronic switches, imaging and storage and photosensitive media(e.g., films, polymers, tapes, slides, crystals and liquid crystals),photorefractive devices, displays, optical disks, digital versatiledisks, amperometric and potentiometric electrodes, ion-selectiveelectrodes, field effect transistors, interdigitated electrodes andother capacitance-based devices, piezoelectric and microgravimetricdevices, surface acoustic wave and surface plasmon resonance devices,thermistors, and the like. These and other transducers, transductionprinciples and related devices are known to those of skill in the art(e.g., Taylor, R F (1990) Biosensors: Technology Applications andMarkets, Decision Resources, Inc., Burlington, Mass.), as are techniquesfor coupling artificial photosynthesis to electrical, electronic andoptoelectronic devices (e.g., Gust et al. (1994)). Phycobilisomeproperties, energies or activities that can be functionally coupled to atransducer include, without limitation, mass, photon absorption oremission, specific binding, catalytic and other signal-generatingactivities using phycobilisome conjugates, reconstitution anddissociation reactions, and energy transfer to or from molecular specieswhich are functionally coupled to the phycobilisome or phycobilisomecomplex (e.g., by electronic coupling, preferably by intimateintermolecular proximity and more preferably by covalent attachment, oralternatively by mass or energy transfer accompanying noncovalentinteractions such as specific binding).

[0136] Transducers of the instant invention typically comprise anorganic or inorganic solid support, matrix or surface to whichphycobilisomes can be attached either directly or through conductive,reflective, transmissive or passive intermediate(s) (e.g., a wire, lead,fiber, connector, interface, layer, channel or conduit). Transducersurfaces include, without limitation, inorganic substrates such assilicon, silica, silicates, plastics, polymers, graphite and metals usedin microfabrication of integrated circuits; glasses, plastics, polymersand quartz as used in optical fibers, planar waveguides and opticaldisks; thin and thick films and organic and inorganic monolayers,bilayers, multilayer stacks, membranes, polymers and coatings as used insemiconductors, field effect transistors, photoelectric devices andsensors; and microparticles, microvesicles, lipid bilayers, dendrimers,nanostructures, and biocompatible polymers as used in diagnostics, drugdelivery and medical devices.

[0137] Attachment surfaces may be modified by covalent and noncovalenttechniques such as photochemical coupling, plasma treatment, chemicaletching, chemical grafting and micromachining processes which arewell-known in the art such as lithography, thin film deposition, wet anddry substrate etching, plating, bonding, fusion, templating, injectionmolding, and the like. Phycobilisomes, phycobilisome complexes andconjugates may be localized at or near a transducer surface by methodsincluding, but not limited to, covalent attachment, hybridization,specific binding, adsorption, encapsulation, controlled deposition,self-assembly or reconstitution of partially dissociated phycobilisomesor isolated constituents in the presence or absence of an immobilizedphycobiliprotein linker polypeptide or anchor polypeptide.Alternatively, a phycobilisome constituent (e.g., a linker polypeptideor anchor polypeptide) or a ligand or receptor (e.g., a peptide ornucleic acid) can be synthesized on a surface in situ (e.g., Fodor etal., Science, 251:767-772 (1991), Pirrung, et al. (1994), “Preparationof oligonucleotide arrays for hybridization studies,” Human GenomeProgram, U.S. Department of Energy, Contractor-Grantee Workshop III,Feb. 7-10, 1993, p. 173) followed by affinity-based attachment of aphycobilisome. In addition to surface attachment, phycobilisomes may beincorporated or encapsulated within a transducer, e.g., a microvesicle,microparticle, liposome, monolayer, membrane, film, gel or polymer.Phycobilisomes embedded, entrapped or incorporated in this manner can beused to transfer mass, energy, electrons or photons or perform usefulwork across a membrane or within a segregated phase, environment orvessel. Methods for embedding, entrapping and attaching substances usinglipids, micelles, liposomes, membranes and membrane mimetics are wellknown in the art (U.S. Pat. Nos. 3,966,580 (1976) and 4,490,216 (1984),Betageri et al. (1993), Gregoriadis (1993), Guo et al. (1990), Fendler(1982), Janoffet al. (1988), Machy et al. (1987)).

[0138] Functional coupling between a phycobilisome of the invention anda transducer can occur by the transfer of mass, energy, electrons orphotons or by coupled chemical or enzymatic reactions that share acommon intermediate, mediator or shuttle species. In a preferred mode ofoperation, a phycobilisome complex or conjugate comprises aphotosynthetic reaction center which is functionally coupled to thetransducer. A phycobilisome complex comprising a photosynthetic reactioncenter can be functionally coupled to a transducer by energy transferand preferably electronic coupling of the charge-separated state of thereaction center. Alternatively, for phycobilisomes lacking a reactioncenter (e.g., a subassembly or rod), site-specific methods can be usedto attach an artificial reaction center (e.g., a signal-generatingmolecule, complex, or group of molecules, capable of producing acharge-separated state) within energy transferring distance of thephycobilisome terminal acceptor. In this case, the phycobilisome can befunctionally coupled to an artificial reaction center which can furtherbe coupled to a transducer by electronic coupling or energy transfer.Functional coupling of phycobilisome complexes and phycobilisomes withartificial reaction centers to transducers can also be achieved orimproved using additional coupled signal-generating molecule(s) (e.g., aphotosystem, enzyme, cofactor, or molecular mimic). Low molecular weightpigments, donors and acceptors can also be used as mediators or shuttlespecies to enable or enhance functional coupling to transducerscomprising coatings, films, polymers, membranes, monolayers and the like(e.g., Kuhn et al. (1979)).

[0139] The invention disclosed herein provides functional coupling ofphycobilisomes and phycobilisome complexes to signal-generatingmolecules and transducers, thereby enabling phycobilisomes andphycobilisome conjugates to serve as optoelectronic components thatmimic the light-harvesting efficiency of photosynthetic antenna systems.Since the light harvesting activity of phycobilisomes can be modulatedby ambient conditions (e.g., ionic strength, pH, solvents, temperature,moisture, light) and since phycobilisomes can be functionally coupled tosignal-generating molecules capable of reporting local events orconditions (e.g., through energy or electron transfer, catalysis orspecific binding), phycobilisome-based biotransducers can serve assensors and actuators responsive to a wide range of conditions, events,ligands, receptors, and signals.

[0140] Use of synthetic antenna structures in artificial photosynthesishas been reported (Gust et al. (1993)). Methods have also been describedto interface artificial reaction centers with nonbiological structuressuch as liposomes, micelles, Langmuir-Blodgett films and polymers aswell as photoelectric devices such as molecular photodiodes andphotelectrochemical cells (Fujihira M (1991), “Photo-electric conversionwith Langmuir-Blodgett films,” In: Honda K (Ed.) Photochemical Processesin Organized Molecular Systems, Elsevier Science Publishers, Amsterdam,pp. 463-482; Wang, et al. (1992), “Light-induced electron transfer ofporphyrin triad for photoelectric conversion,” J. Phys. Chem.,96:2886-2891), nanoscale wires (Kittlesen, et al. (1984), “Chemicalderivatization of microelectrode arrays by oxidation of pyrrole andN-methylpyrrole: Fabrication of molecule-based electronic devices,” J.Am. Chem. Soc., 106:7389-7396), nanofabricated electrodes and conductingsubstrates (Gust et al. (1994)). This invention provides for theimprovement whereby natural photosynthetic structures can be integratedwith synthetic devices, i.e., through functional coupling ofphycobilisomes to such nonbiological transducers.

[0141] Phycobilisome-based assays according to this invention can bedetected electrochemically as well as fluorometrically, for examplethrough “phycobilisome electrodes,” as alternatives to enzyme electrodescommonly used in amperometric immunosensors. In addition, directionaland intimate coupling of phycobilisomes to well-establishedmicroelectronic devices (e.g., photodiodes, charge-coupled devices) canprovide means for efficient photoelectronic signal transduction on asubmicron scale. Within the contemplation of this invention aremicrominiaturized “biotransducers” such as photoelectric converters,transistors, switches and amplifiers responsive to directional lightenergy transfer from immobilized, structurally oriented phycobilisomes.

IMMOBILIZATION EXAMPLE 1 Modified Phycobilisomes Immobilized onto LatexMicrospheres

[0142] FA-treated phycobilisomes and phycobilisome-antibody conjugates(“modified phycobilisomes”) quenched with lysine and purified by gelchromatography were immobilized on uniform latex particles eithercovalently or by passive adsorption. All incubations were performed atroom temperature with rotation. Fluorescent and nonfluorescentcarboxylate-modified latex microspheres ranging in diameter from 0.03-1uM were used at final concentrations of 1-10 mg/ml.

[0143] Passive adsorption to microspheres was performed for 1-16 hoursin 100 mM phosphate (pH 7.2) at immobilization ratios (μg protein/mgparticle) ranging from 20-200 μg/mg. Modified phycobilisome-latexsuspensions were washed by repeated centrifugation at 8000×g in 100 mMKPi containing 150 mM sodium chloride.

[0144] Covalent immobilization was performed at the sameprotein/particle ratios in a one-step procedure using1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDAC) in 100 mM MES (pH6.8). Modified phycobilisomes were rapidly spiked into the particlesuspension with mixing, allowed to react for 1-2 hours and washed bycentrifugation.

[0145] For prolonged storage, immobilized phycobilisomes werepost-treated with 1% FA in 100 mM KPi (pH 7.4), quenched with lysine,reduced with sodium cyanoborohydride and washed with 100 mM KPicontaining 150 mM sodium chloride and 0.05% sodium azide.

IMMOBILIZATION EXAMPLE 2 Antigens and Antibodies on ParamagneticParticles

[0146] Immobilizations were performed at room temperature according tothe following protocol. Amine-modified BIOMAG (Advanced Magnetics) waswashed five times with vigorous vortexing and magnetic separation in 10mM sodium phosphate (NaPi; pH 7.35) at a particle concentration of 5-10mg/ml. After the final wash, the wet cake was resuspended to 25 mg/ml in6.25% GA (Sigma) and rotated at room temperature for 3 hours. GA-treatedparticles were washed six times in NaPi. Washed, GA-activated particleswere resuspended with PBS (pH 7.2-7.4) containing the protein to beimmobilized at 3-10 mg/ml to yield 100-160 ug protein per mg BIOMAG. BSAwas included as a doping agent to adjust the spacing of immunoreactantson BIOMAG particles. An aliquot of the protein solution was retained fordetermination of immobilization efficiency. The protein-particle slurrywas rotated at room temperature for 16-24 hours. Particles weremagnetically separated. The supernatant was decanted and retained forestimation of residual protein. Unreacted GA groups were quenched byresuspension of particles to about 10 mg/ml in 1 M glycine (pH 8.0)followed by rotation for one hour. Quenched particles were washed twicein PBS (pH 7.4) and blocked by rotation for two to four hours in PBScontaining 2 mg/ml BSA. Blocked particles were washed three times in PBScontaining 1 mg/ml BSA, resuspended to a particle concentration of 10mg/ml and stored at 2-8° C. Working aliquots were washed three times inassay buffer with thorough vortexing at a particle concentration ofabout 1 mg/ml prior to use to protect against leaching of immobilizedreagents with prolonged storage.

IMMOBILIZATION EXAMPLE 3 Antigens and Antibodies Immobilized ontoMicrotiter Wells

[0147] Proteins were passively adsorbed to surface-modified polystyrenemicrotiter plates by passive adsorption according to the followingprotocol. Antigens and antibodies were diluted to 2-20 ug/ml in 50 mMcarbonate buffer (pH 9.6) or 10 mM sodium phosphate (pH 7.4) inborosilicate glass tubes or 50 ml polypropylene centrifuge tubesimmediately before use. Clear polystyrene IMMULON™-4 (Clear polystyrene96-well microtiter plates) or white MICROLITE™ 2 (opaque whitepolystyrene 96-well microtiter plates) flat-bottomed microtiter plates(Dynatech) were coated at 100 ul per well for 2 hours at 37° C., 4 hoursat room temperature (20-23° C.) or 15-24 hours at 2-8° C. Plates weredecanted and washed once by filing wells with wash buffer (PBS (pH 7.4)containing BSA at 1 mg/ml) and decanting. Wells were blocked for 1 hourwith 200 μl PBS containing 2 mg/ml BSA and washed five additional timeswith wash buffer.

ASSAY EXAMPLE 1 Competitive Immunoassay With Photometric Detection

[0148] Fifty microliters of sample (assay buffer with or without varyingconcentrations of mouse immunoglobulin (MIgG)) was added to 12×75 mmglass test tubes arranged in a MAGIC™ (paramagnetic particles) separatorunit with a side-pull magnetic base (Corning). One hundred microlitersof freshly washed BIOMAG-MIgG was added at particle concentrationsranging from 0.3-10 mg/ml. Tubes were vortexed, and 50 ulphycobilisome-GAM conjugate (molar ratio of 1.5-18 GAM/phycobilisome)was added at phycobilisome concentrations ranging from 1-100 ug/ml(5-500 mAU/ml). The reaction mixture was vortexed and incubated for onehour at room temperature. Particles were separated by placing the Magic™rack on its magnetic base for five minutes. One hundred sixty microliteraliquots of assay supernatants were transferred to 12×75 mm glass testtubes and subsequently diluted with 100 mM KPi (pH 7.35) to 1 ml forphotometric assays or 3 ml for fluorometric assays.

[0149] Data presented below represent a checkerboard co-titration ofphycobilisome-GAM conjugate and BIOMAG-MlgG, demonstrating that bindingis solid phase limited. Percent binding increased dramatically withincremental increases in particle concentration. Supernatant Absorbance(mAU/ml) % binding at [BIOMAG] = PB-GAM MIgG BIOMAG = 30 BIOMAG = 100BIOMAG = 300 30 100 300 (ug/test) ug/test ug/test ug/test ug/testug/test ug/test ug/test 40 10 210 212 213 40 0 210 200 173 0.0 4.7 18.812 10 66 68 66 12 0 63 54 44 4.5 20.6 33.3 3 10 12 12 12 3 0 12 10 4 0.016.7 66.7

[0150] In separate experiments, conjugate binding was dramaticallyincreased by working at 10-fold higher concentrations of conjugate andsolid phase. Assay sensitivity was determined to be below 100 ng/mlMIgG.

ASSAY EXAMPLE 2 Competitive Immunoassay Using Fluorescent Detection

[0151] Assays were performed according to the methods of example 6, butreagent concentrations were adapted for fluorescent detection. Datapresented below were obtained using 250 ng per test of phycobilisome-GAMconjugate and 250 μg per test of BIOMAG-MIgG. Fluorescence was recordedusing 545 nm excitation. [MIgG] (ng/test) E₆₆₆ (cps × 10⁻⁵) % boundinhibition (cps × 10⁻⁵) 0 3.74 24.3 — 1 4.00 19.0 0.26 10 4.39 11.1 0.65100 4.90 0.8 1.16 1,000 4.94 0.0 1.20

ASSAY EXAMPLE 3 Displacement Assay Using Phycobilisome ConjugatePrebound to Immobilized Antigen

[0152] Washed BIOMAG-rabbit IgG (BIOMAG-RIgG) was pretreated withphycobilisome-GAM conjugate (molar ratio of 5/1 GAM/phycobilisome) fortwo hours at room temperature with mixing. The prebound reagent mixturewas washed three times in assay buffer and resuspended to a particleconcentration of 400 ug/ml. Five hundred microliter aliquots of preboundreagent were added to 12×75 mm test tubes. The assay was performed byadding 50 ul of sample (buffer with or without MIgG) to the mixture,vortexing, and incubating at room temperature for 60 minutes. Aftermagnetic separation, 500 ul of supernatant was transferred to 2.5 mil 0.I M M for fluorescence measurements. Fluorescence (cps × 10⁻⁵) % ofmaximal [MIgG] (ng/test) E⁶⁶⁶ displacement displacement 0 10.53 — 110.72 0.19 6.1 10 10.85 0.32 10.4 100 11.62 1.09 35.3 1,000 12.46 1.9362.5 10,000 13.62 3.09 100.0

[0153] A microtiter plate assay in displacement format using the samephycobilisome-GAM conjugate prebound to RIgG-coated wells (20 ug/ml)yielded similar results. The lower displaceable signal is due to thelower solid phase binding capacity of microtiter wells compared toparamagnetic particles. Fluorescence (cps × 10⁻⁵) % of maximal [MIgG](ng/test) E⁶⁶⁶ displacement displacement 0 3.43 — 1 4.11 0.68 36.8 104.78 1.35 73.0 100 5.25 1.82 98.4 1,000 5.28 1.85 100.0

ASSAY EXAMPLE 4 Sandwich (Immunometric) Immunoassay

[0154] Reverse sandwich assays were performed by preincubating MIgG withphycobilisome-GAM conjugate followed by capture ofphycobilisome-GAM-MIgG complexes with BIOMAG-rabbit anti-mouse antibody(BIOMAG-RAM). This protocol maximizes assay sensitivity by allowing theprimary (dynamic) immunoreaction to proceed in solution, improving assaykinetics and minimizing steric constraints. Alternatively,phycobilisome-GAM conjugate was used as a labeled second antibody todetect monoclonal antibody binding to immobilized rabbit IgG (RIgG) asfollows.

[0155] Fifty microliters of buffer or mouse anti-rabbit antibody (MAR)was preincubated with 50 ul phycobilisome-GAM conjugate (20-80 ug/ml)for 30 minutes. Immune complexes were captured by addition of 100 ul offreshly washed BIOMAG-RIgG at a particle concentration of 10 mg/ml. Thereaction was allowed to proceed for 60 minutes prior to magneticseparation. Fluorescence measurements were performed followingdilution/transfer of 160 ul assay supernatant to 2.84 ml 0.1 M KPi.[MAR] 1 ug/test PBsome-GAM 2 ug/test PBsome-GAM 4 ug/test PBsome-GAM(ng/test) E₆₆₆× 10⁻⁶ % bound E₆₆₆× 10⁻⁶ % bound E₆₆₆× 10⁻⁶ % bound 01.483 0 2.400 0 4.147 0 0.1 1.392 6.1 2.322 3.3 4.196 0 1.0 1.142 23.01.786 25.6 3.430 17.3 10 0.823 44.5 1.289 46.3 2.107 49.2 100 0.697 53.00.992 58.7 1.709 58.8 1000 0.615 58.5 0.967 59.7 1.511 63.6

ASSAY EXAMPLE 5 Microtiter-Based Immunoassay With Visual Detection

[0156] Competitive Assays: White polystyrene MICROLITE™ 2 microtiterplates (Dynatech) were coated by passive adsorption for 15 hours at 2-80C with 2-20 ug/ml MIgG in 10 mM sodium phosphate (pH 7.35). Supernatantswere aspirated. Wells were incubated for 60 minutes at room temperaturewith 200 ul blocking buffer (10 mM phosphate-buffered isotonic saline(PBS, pH 7.4) containing 100 mM potassium phosphate (pH 7.35), 2 mMsodium azide and 2 mg/mil BSA) and washed six times with 250 ul washbuffer (PBS containing 1 mg/ml BSA). After the final wash, plates wereinverted on paper towels and drained by blotting vigorously. Fiftymicroliters of assay buffer (PBS containing 100 mM potassium phosphate(pH 7.35), 2 mM sodium azide and 1 mg/ml BSA) or MIgG (10-1000 ng/wellin assay buffer) was added to each well followed by 50 ul ofphycobilisome-GAM at 0.5-10 ug/well. Plates were incubated for one hourwith shaking at room temperature, decanted, and inspected before andafter washing three times with assay buffer. Phycobilisome-GAM bindingto immobilized MIgG could be visually discriminated (both before andafter plates were washed) as a purplish-pink coating on the bottom andlower insides of wells under the following conditions:

[0157] 1. MIgG coating concentration>0.5 ug/well; and

[0158] 2. phycobilisome-GAM conjugate>1 ug/well; and

[0159] 3. competing [soluble MIgG]<10 ng/well.

[0160] Significant nonspecific binding (bound color at 1 ug/well solubleMIgG) was not visibly apparent in washed plates even at the highestconcentrations of phycobilisome-GAM. Visually detectable specificbinding (color difference ±1 g/well MIgG) was most dramatically apparentin wells treated with the highest coating and conjugate concentrations(10-20 ug/ml coating×5-10 ug/well phycobilisome-GAM). Under theseconditions, the visual detection limit for MIgG was 10-100 ng/test,corresponding to 101-2-10-13 moles/test (about 10⁻⁹ M MIgG).

[0161] Sandwich Assays: White polystyrene MICROLITE™ 2 microtiter plates(Dynatech) were coated for 15 hours at 2-8° C. with 2-20 ug/mlaffinity-purified RAM (H+L) antibody in 10 mM sodium phosphate (pH7.35). Supernatants were aspirated and wells were incubated with 200 ulblocking buffer (as per competition assays) for one hour at roomtemperature followed by six washes with 250 ul wash buffer (PBScontaining 1 mg/ml BSA). After the last wash, plates were inverted anddrained on paper towels with vigorous blotting. One hundred microlitersof assay buffer or MIgG (10-1000 ng/well in assay buffer) was added toeach well, incubated for one hour at room temperature and aspirated.Wells were washed three times with 250 ul wash buffer. Phycobilisome-GAMconjugate was added at 0.5-10 ug/well in 100 ul assay buffer, incubatedfor two hours at room temperature with shaking, decanted, and inspectedbefore and after three was with assay buffer. With and without washing,bound phycobilisome-GAM could be visually discerned in wells exposed toMIgG under the following conditions:

[0162] 1. RAM coating at >0.2 μg/well; and

[0163] 2. [MIgG]>10 ng/well; and

[0164] 3. [phycobilisome-GAM] at 1.5-10 μg/well, depending on RAM andMIgG concentrations.

[0165] Prior to washing, visual discrimination of wells exposed to 10ng/ml MIgG compared to assay buffer was marginal. Washing provided onlya minor improvement in resolution. No effort was made to optimize thevisual detection limit of immunometric microtiter assays by increasingsolid phase binding capacity or conjugate concentration, selecting ahigher affinity tracer antibody, modifying the assay protocol or buffercomposition, or determining preferred conditions for inspection of thebound phase under UV illumination.

ASSAY EXAMPLE 6 Immunochromatographic Dipstick With Visual Detection

[0166] Competitive Assay Configuration: MIgG was covalently immobilizedto localized zones on aldehyde-treated modified polysulfone membranes asfollows. ULTRABIND™ (modified polyethersulfone affinity membrane) US800unsupported membrane with an effective pore size of 0.8 uM (GelmanSciences) was cut into 20 cm×6 cm sections. MIgG (2-10 mg/ml in 10 mMphosphate-buffered isotonic saline (PBS), pH 7.2, containing 0.1% sodiumazide) was manually spotted by graduated capillary pipet (DrummondScientific) at 4 ul per linear centimeter along a longitudinal linepencilled midway across each section (3 cm from either edge). After airdrying for 30 minutes, membranes were incubated with gentle shaking forone hour at room temperature in 50 ml blocking buffer consisting of 1%BSA in 10 mM PBS (pH 7.4), rinsed twice in 100 ml PBS (pH 7.2)containing 0.1% BSA and air dried for 3 hours. Rinsed, dried membraneswere then washed for one hour with shaking in PBS (pH 7.2) containing0.2% Tween 20 and allowed to dry overnight at room temperature.

[0167] Phycobilisome-GAM conjugate was applied to MIgG-modifiedmembranes as follows. Dry, washed membrane sections were cut width-wiseinto 1×6 cm strips. Ten microliters of phycobilisome-GAM conjugate (2.5AU₅₄₅/ml) comprising approximately 0.5 mg/ml stabilized P. cruentumphycobilisomes and 10 ug/ml immunologically active GAM in 0.5 M KPi (pH7.35) containing 0.1 M sucrose was applied over about 1 squarecentimeter of each 1×6 cm strip midway between one end and the centraltransverse line of immobilized MIgG. Conjugate-treated strips wereair-dried for 30 minutes before use.

[0168] Immunochromatographic MIgG dipsticks were evaluated by contactingthe conjugate-treated ends of dried strips to buffer (PBS (pH 7.4)containing 1 mg/ml BSA) or MIgG (1 ug/ml in buffer) and allowing samplesto wick up strips by capillary action. When the fluid front had migrated3.5 cm up the buffer-treated strip (about 10 minutes), a purple-pinkband appeared at the immobilized MIgG line (3 cm) and grew progressivelymore intense as the strip became entirely saturated with buffer (about20 minutes). No band was apparent in strips exposed to MIgG-containingbuffer, indicating that binding of phycobilisome-GAM to immobilized MIgGwas substantially inhibited by soluble MIgG.

[0169] Inspection of strips in a darkroom under long-wavelength (365 nm)ultraviolet illumination failed to reveal localized phycobilisome-GAMfluorescence in MIgG-treated dipsticks. In buffer-treated dipsticks,phycobilisome-GAM bound to immobilized MIgG was apparent as an intense,fluorescent-red band against a dark blue background. This fluorescentband disappeared after strips were air-dried. When water was applied tothe visible band on dry, buffer-treated strips, intense localized red(phycobilisomes) and mobile orange (B-PE) fluorescent phases wereobserved, suggesting partial dissociation of GA-treated phycobilisomeswith drying and re-wetting. Similar results were obtained byfluorometric evaluation of phycobilisome-GAM conjugates before and afterfreeze-drying. The ratio of 666/573 nm emission with 545 nm excitationdecreased markedly with drying and reconstitution, suggestingsignificant uncoupling of fluorescence energy transfer, unlessconjugates were pretreated with sucrose or other protectants. Sinceisolated B-PE is a more intense fluorophore than APC (the terminalacceptor of P. cruentum phycobilisomes), dissociation of phycobilisomesbetween conjugate binding and detection steps provides a means toamplify the fluorescent signal and increase assay sensitivity.

[0170] Sandwich Assay Configuration: Immunometric MIgG dipsticks wereprepared by methods substantially equivalent to those for competitivedipsticks, except affinity-purified RAM antibody ((H+L chain)-specific;OEM Concepts) was immobilized to ULTRABIND™ US800 membranes in place ofMIgG. Ten microliters of RAM (2 mg/ml) per linear centimeter was spottedwidth-wise across 10×6 cm membrane sections, which were then blocked,rinsed, washed and cut into 1×6 cm strips as per MIgG-immobilizedmembranes. Ten microliters of phycobilisome-GAM conjugate (5.1 AU₅₄₅/ml)comprising approximately 1 mg/ml stabilized P. cruentum phycobilisomesand 20 ug/ml immunologically active GAM in 0.5 M KPi (pH 7.35)containing 0.2 M sucrose was applied midway between one end and theimmobilized RAM line as per competitive dipsticks, and strips wereair-dried before use.

[0171] Sandwich MIgG dipsticks were evaluated by contacting theconjugate-treated end to PBS-BSA buffer with or without MIgG (1 ug/ml)and allowing the sample to saturate strips by capillary action (about 20minutes). A distinct purple-pink band formed at the immobilized RAM linein MIgG-treated dipsticks, but not in buffer-treated controls. Theseresults demonstrate specific binding of a soluble phycobilisomeconjugate in an immunometric assay with a visual detection limit below6×10⁻⁹ M.

ASSAY EXAMPLE 7 Direct Quantification of Bound Oligonucleotide

[0172] A synthetic oligonucleotide is produced by either PCR or use of anucleic acid synthesizer. An amine group is introduced on the end ofthis by a standard method. This amine is then biotinylated using NHSester linked biotin reagents (e.g., Pierce Chemical's sulfo-NHS-biotin).The biotinylated oligonucleotide is diluted in buffer in a serial mannerand then placed on nitrocellulose or other solid media commonly used fornucleic acid transfer (e.g., nylon or supported nitrocellulose). This isdone either by dotting on a known amount of material or using anapparatus made for quantitative transfer of nucleic acid such as a dotor slot blotter. The material is then covalently linked to the solidphase using either UV crosslinking or drying in a vacuum oven at 85° C.This is then blocked with materials to prevent nonspecific binding ofthe labeled binding reagents. Phycobilisomes conjugated directly tostreptavidin or avidin as described above are then added to a buffer andprovided to a blot containing the immobilized, biotinylated nucleicacid. These are allowed to react with gentle shaking to allowinteraction of biotin and streptavidin. Blots are then washedextensively in buffers with or without the addition of materials tofacilitate release of nonspecifically bound materials. The boundmaterial is then visualized either directly or with an instrument tofacilitate photometric or fluorometric detection.

ASSAY EXAMPLE 8 Indirect Quantification of Bound Oligonucleotide viaHybridization

[0173] A synthetic oligonucleotide (A) and its complementary strand (A′)are produced by either PCR or use of a nucleic acid synthesizer. Thetest oligonucleotide (A) is diluted in buffer in a serial manner andthen placed on nitrocellulose or other solid media commonly used fornucleic acid transfer (e.g., nylon and supported nitrocellulose). Thisis done either by dotting on a known amount of material or using anapparatus made for quantitative transfer of nucleic acids such as a dotor slot blotter. The material is then covalently linked to the solidphase using either UV crosslinking or drying in a vacuum oven at 85° C.This is then blocked with materials to prevent nonspecific binding ofthe labeled binding reagent. An amine group is introduced on the end ofthe complementary strand (A′) by a standard method. This amine is thenbiotinylated using NHS ester linked biotin reagents (e.g., PierceChemical's sulfo-NHS-biotin). The biotinylated complementary strand isthen hybridized with the immobilized test strand using any of thestandard hybridization techniques. The blot is washed well to remove thefree biotinylated probe and then reacted with a secondary labelingsystem using phycobilisomes labeled with streptavidin or avidin.Phycobilisomes conjugated directly to streptavidin or avidin asdescribed above are then added to a buffer and provided to a blotcontaining the specifically bound, biotinylated complementaryoligonucleotide. These are allowed to react with gentle shaking to allowinteraction of biotin and streptavidin. Blots are then washedextensively in buffers with or without the addition of materials tofacilitate release of nonspecifically bound materials. The boundmaterial is then visualized either directly or with an instrument tofacilitate photometric or fluorometric detection.

ASSAY EXAMPLE 9 Use in DNA Blotting (Southern) Hybridization

[0174] Large molecular weight DNA is transferred to nitrocellulose orother similar solid phase material commonly used for DNA transfer. Thisis done using either capillary, electrophoretic or vacuum methods oftransfer. The DNA is fixed using UV or heat as normally done. This isthen hybridized with a biotinylated probe to a specific DNA sequence at65° C. to allow the complementary probe to bind to the target sequence.This is washed to remove nonspecifically bound DNA, and the blot isreacted with avidin- or streptavidin-labeled phycobilisomes tospecifically label hybridized biotinylated probes. This is washed toremove nonspecifically bound material and visualized by eye or byphotometric or flurometric instrumentation. This type of assay can alsobe done using protein/antibody or receptor/ligand links in place of theavidin/biotin links.

ASSAY EXAMPLE 10 Use in RNA Blotting (Northern) Hybridization

[0175] RNA blots are probed in a manner analogous to that described forDNA. In this case either a synthetic DNA or RNA oligonucleotide is usedas the probe and is labeled either directly or indirectly withphycobilisomes.

ASSAY EXAMPLE 11 Use in Protein Detection (Western Blotting)

[0176] After protein electrophoresis, the protein is transferred tonitrocellulose or other solid matrices using electric current fortransfer. The protein is then detected either directly using aphycobilisome conjugated to an antibody against the target protein orindirectly using a phycobilisome attached to biotin or anti-antibody asa secondary label.

ASSAY EXAMPLE 12 Enhancement of Signal Using Deterioration(Dissociation) of the Phycobilisome

[0177] When not concerned with Stokes shift, signal enhancement may beobtained by proceeding with the binding and removal of nonspecificbinding as in Assay Example 11. Then the sample is exposed to distilledwater to break down the phycobilisome into constituentphycobiliproteins. Freed phycobiliproteins then are free toflourescently emit light at their own emission maximum versus beingfunneled through a terminal emitter such as allophycocyanin.

[0178] Phycobilisomes isolated from Porphyridium cruentum, which arecomposed mostly of phycoerythrin, were conjugated to goat anti-mouseantibody (GAM). Mouse IgG was immobilized in a strip on a small piece ofULTRABIND 800™ (Gelman) using the activated groups on the membrane forcovalent attachment of the mouse IgG. This was dried, blocked with BSA,dried again, then used in a dipstick format in the test systemcontaining the phycobilisome-GAM. A line of conjugate was placed nearthe bottom of the paper after protein blocking was done and allowed todry. The paper was dipped in a buffer (containing phosphate, salt and asmall amount of BSA) and as the buffer passed the dried-on conjugate,the conjugate was completely solubilized and moved cleanly over thecovalently bound mouse IgG. The conjugates bound to the mouse IgG, andwhat was not bound was removed by a wash in the loading buffer. This wasvisualized using a ultraviolet lamp and very nice red color was observedon the band where the mouse IgG had been immobilized. If the paper wasallowed to dry and then distilled water was placed on the paper, a rapidchange in fluorescent emission was seen as the phycobilisome broke downand B-PE emission became dominant. This was a much more intense colorthan that seen using the intact phycobilisome. The exact amount ofamplification was not determined.

ENERGY TRANSDUCTION EXAMPLE 1 Biotransducer Comprising a PhycobilisomeFunctionally Coupled to an Optical Fiber

[0179] Phycobilisomes isolated from P. cruentum and stabilized with FAare site-specifically labeled hear the terminal acceptor of the corecomplex using affinity purified rabbit anti-APC antibody (RAAPC;Accurate Chemical & Scientific Corporation, Westbury N.Y.). Affinitypurified goat anti-rabbit IgG (GAR; OEM Concepts, Toms River, N.J.) isimmobilized on 1×60 mm cylindrical quartz fibers with polished ends bypassive adorption in a PBS buffer for at least two hours at roomtemperature. (In an alternative mode of operation, GAR is covalentlyattached through carbohydrate groups in the Fc region tohydrazide-modified fibers, thereby maximizing the immunologicavailability of antigen-combining sites.) Coated fibers are washedthoroughly in PBS-BSA and air-dried prior to use in binding assays.Specific binding of the RAAPC-phycobilisome conjugate to GAR-coatedfibers is detected through evanescent excitation of bound phycobilisomesand evanescent capture of emitted energy using a portable fluorometer(ORD Inc., North Salem, N.H.) equipped with 550 nm excitation and 660 nmemission band-pass filters. Fibers are mounted vertically in a flow cellhaving a capacity of 46 ul and perfused with PBS-BSA at a rate of 184ul/minute. Fluorescent light is collected and guided by the fiber anddetected by photodiodes arranged so as to distinguish betweensurface-bound fluorescence (from smaller angles) and background light(from larger angles). Evanescent detection principles for both planarwaveguides (e.g., Badley, et al. (1987), “Optical biosensors forimmunoassays: the fluorescence capillary-fill device,” Phil. Trans. R.Soc. Lond., B316: 143-160) and optical fibers (e.g., Rogers, et al.(1992), “Fiber-Optic biosensors based on total internal-reflectionfluorescence,” In: Biosensor Design and Application, (Eds. P. R.Mathewson and J. W. Finley), Am. Chem. Soc. Symp. Ser., 511, Chapter 13,pp. 165-172) are well-known in the art. The transducer in this exampleis the optical fiber operatively coupled through its evanescent field tophotodiode(s) capable of generating an electronic signal (voltage).RAAPC-phycobilisome binding to the GAR-coated fiber is dose-dependentand competitively inhibited by either unlabeled GAR or RAAPC antibodies.This example therefore illustrates a fiberoptic sensor that relies onfunctional coupling of a phycobilisome to a transducer for detection ofan antibody.

[0180] A phycobilisome-based biotransducer relying on regio-specificattachment and functional coupling of phycobilisomes to an optical fiberis prepared and used as follows. Anchor polypeptide is isolated bycomplete dissociation and column chromatography from P. cruentumphycobilisomes and passively adsorbed to quartz fibers. The rod-corelinker polypeptide is also isolated from P. cruentum phycobilisomes bydissociation and chromatography and is biotinylated by establishedmethods using a long-chain N-hydroxysuccinimide ester of biotin (PierceChemical Company, Rockford, Ill.). APC-containing core complexes arethen reconstituted on anchor protein-coated quartz fibers from isolatedphycobiliproteins and linker polypeptides. The reconstituted,immobilized core complexes are then crosslinked in place using GA(0.05-0.50%). Excess GA is removed by repeated washes with PBS.Streptavidin (2-50 ug/ml in PBS) is then conjugated to reactive aldehydegroups on the immobilized core complexes. Fibers are then quenched withlysine, blocked with PBS-BSA, washed extensively and air-dried. ModifiedP. cruentum phycobilisomes comprising a single rod are reconstitutedfrom isolated phycobiliproteins, intra-rod linker polypeptides andbiotinylated rod-core linker polypetides. These reconstituted rods,having a biotinylated rod-core linker polypeptide near the terminalacceptor, are then stabilized, quenched and reduced using FA, lysine andsodium cyanoborohydride (cf. “Detailed Description of PreferredEmbodiments” supra). Specific binding of stabilized, biotinylatedphycobilisome rods to streptavidin-modified immobilized core complexesis measured by evanescent excitation and detection using 550 nm and 660nm band-pass filters as described above. In the absence of unlabeledbiotin, specific binding of biotinylated rods to streptavidin-modifiedimmobilized core complexes results in efficient evanescent excitation at550 nm and collection of emitted fluorescence at 660 nm. Unlabeledbiotin added to the flow cell competitively inhibits binding of thebiotinylated rods, interrupting evanescent excitation. Unlabeled avidinor streptavidin also competitively inhibits specific binding andevanescent excitation. This phycobilisome-based biotransducer thereforeserves as a prototypical example of an optoelectronic sensor capable ofdetecting either ligands (i.e., biotin and derivatives) or receptors(i.e., streptavidin, avidin and derivatives). Optimal performance ofthis phycobilisome-based fiberoptic sensor requires regio-specificconjugation to phycobilisomes (i.e., biotinylation of rods) and/orregio-specific attachment of phycobilisomes to transducers (i.e.,immobilization of core complexes). Site-specific attachment enablesdirectional energy transfer and functional coupling to the transducer.Similar “reconstitution-based” sensing principles can be developed usingeither algal or cyanobacterial phycobilisome subassemblies prepared,e.g., by partial dissociation using methods adapted from Rigbi et al.(1980), Gantt et al. (1979) and Nies et al. (1981) with or withoutcovalent stabilization.

ENERGY TRANSDUCTION EXAMPLE 2 Biotransducer Comprising a PhycobilisomeFunctionally Coupled to a Photodiode

[0181] Anchor polypeptide is purified from P. cruentum phycobilisomes asdescribed in Energy Transduction Example 1 and passively adsorbed to thehydrophobic surface (approximately 4 mm²) of polymer coated indiumphosphide photodiodes selected for maximal responsiveness(signal-to-noise ratio) at 600-700 nm. P. cruentum core complexes arethen reconstituted on anchor protein-coated photodiodes by exposing thesurface to a mixture of isolated phycobiliproteins and linkerpolypeptides. The reconstituted, immobilized core complexes are thencrosslinked in place with GA, excess GA is removed by rinsing, andstreptavidin is conjugated to unreacted aldehyde groups on theimmobilized core complexes. Photodiodes are then quenched with lysine,blocked with PBS-BSA, rinsed extensively and air-dried. Biotinylatedrod-core linker polypeptide is prepared by methods described in EnergyTransduction Example 1. Specific binding of biotinylated phycobilisomerods to streptavidin-modified immobilized core complexes is detected aselectrical current following photodiode excitation through a 550/30 nmband pass filter. In the absence of unlabeled biotin, specific bindingof biotinylated rods to streptavidin-modified immobilized core complexesresults in efficient energy transfer from rods to core complexes to thephotodiode, as evidenced by a voltage-dependent current response of thediode. Immobilized core complexes sensitized by specifically bound rodsare functionally coupled to the photodiode, as demonstrated by thedose-dependent increase in current generated by the photodiode whenincreasing concentrations of biotinylated rods are added. Addition ofunlabeled biotin to biotinylated rod samples results in dose-dependentattenuation of photodiode current due to competitive inhibition ofbiotinylated rod binding. Unlabeled avidin and streptavidin alsocompetitively inhibit photodiode output.

[0182] For purposes of clarity of understanding, the foregoing inventionhas been described in some detail by way of illustration and example inconjunction with specific embodiments, although other aspects,advantages and modifications will be apparent to those skilled in theart to which the invention pertains. The foregoing description andexamples are intended to illustrate, but not limit the scope of theinvention. Modifications of the above-described modes for carrying outthe invention that are apparent to persons of skill in medicine,immunology, semiconductors, fluorescence, instrumentation, and/orrelated fields are intended to be within the scope of the invention,which is limited only by the appended claims.

[0183] All publications and patent applications mentioned in thisspecification are indicative of the level of skill of those skilled inthe art to which this invention pertains. All publications and patentapplications are herein incorporated by reference to the same extent asif each individual publication or patent application was specificallyand individually indicated to be incorporated by reference.

1. An isolated, soluble, stabilized phycobilisome comprising a pluralityof phycobiliproteins specifically connected by at least one linkerpolypeptide.
 2. The stabilized phycobilisome of claim 1, wherein saidphycobilisome comprises at least one rod.
 3. The stabilizedphycobilisome of claim 1, wherein said phycobilisome comprises a corecomplex and no peripheral rods.
 4. The stabilized phycobilisome of claim1, wherein said phycobilisome comprises a core complex and at least onedisc.
 5. The stabilized phycobilisome of claim 1, wherein saidphycobilisome comprises an anchor protein.
 6. The stabilizedphycobilisome of claim 1, wherein said phycobilisome comprises at leastone protein encoded by each of at least two different algal strains. 7.The stabilized phycobilisome of claim 1, wherein the phycobilisome isreconstituted from a mixture comprising an isolated phycobiliprotein oran isolated linker polypeptide.
 8. The stabilized phycobilisome of claim1, wherein said phycobilisome has been modified by covalent attachmentof desired chemical moieties.
 9. The stabilized phycobilisome of claim8, wherein said chemical moieties are attached to a particular portionof the phycobilisome.
 10. The isolated, stabilized phycobilisome ofclaim 1, wherein the phycobilisome is functionally coupled to asignal-generating system.
 11. A phycobilisome conjugate comprising aphycobilisome conjugated to a molecular species selected from the groupconsisting of ligands, receptors, and signal-generating molecules,wherein each phycobilisome comprises a plurality of phycobiliproteinsspecifically connected by at least one linker polypeptide, saidmolecular species being attached to a single type of phycobiliprotein, asingle type of linker polypeptide, or an anchor protein.
 12. Thephycobilisome conjugate of claim 11, wherein the molecular speciesselected from the group consisting of ligands, receptors, andsignal-generating molecules is attached to one type of phycobiliprotein.13. The phycobilisome conjugate of claim 11, wherein the molecularspecies selected from the group consisting of ligands, receptors, andsignal-generating molecules is attached to one type of linkerpolypeptide.
 14. The phycobilisome conjugate of claim 11, wherein themolecular species selected from the group consisting of ligands,receptors, and signal-generating molecules is attached to an anchorprotein.
 15. A phycobilisome conjugate comprising a phycobilisomeconjugated to a molecular species selected from the group consisting ofligands, receptors, and signal-generating molecules, wherein eachphycobilisome comprises a plurality of phycobiliproteins specificallyconnected by at least one linker polypeptide, said molecular speciesbeing attached to a particular portion of said phycobilisome.
 16. Thephycobilisome conjugate of claim 11 or claim 15, wherein thephycobilisome is an isolated phycobilisome.
 17. The phycobilisomeconjugate of claim 11 or claim 15, wherein the phycobilisome isstabilized.
 18. The phycobilisome conjugate of claim 11 or claim 15,wherein said phycobilisome comprises at least one protein encoded byeach of at least two different algal strains.
 19. The phycobilisomeconjugate of claim 11 or claim 15, wherein said phycobilisome isreconstituted from a mixture comprising an isolated phycobiliprotein oran isolated linker protein.
 20. The phycobilisome conjugate of claim 11or claim 15, wherein the phycobilisome is functionally coupled to asignal-generating system.
 21. The phycobilisome conjugate of claim 11 orclaim 15, wherein the molecular species is selected from the groupconsisting of streptavidin, avidin, an antibody, a hapten, biotin, adrug, an antigen, a nucleic acid, a carbohydrate, and a lectin.
 22. Anisolated phycobilisome comprising a plurality of phycobiliproteinsspecifically connected by at least one linker polypeptide, saidphycobilisome being non-covalently attached to a molecular speciesselected from the group consisting of ligands, receptors, andsignal-generating molecules, wherein the molecular species is not anantibody which specifically binds said phycobilisome.
 23. The isolatedphycobilisome of claim 22, wherein the phycobilisome is stabilized. 24.The isolated phycobilisome of claim 22, wherein the attachment betweenthe phycobilisome and the molecular species comprises biotin.
 25. Theisolated phycobilisome of claim 22, wherein the molecular species isattached to a single type of phycobiliprotein, a single type of linkerpolypeptide, or an anchor protein.
 26. The isolated phycobilisome ofclaim 22, wherein the molecular species is attached to a particularportion of said phycobilisome.
 27. The isolated phycobilisome of claim22, wherein the phycobilisome is functionally coupled to asignal-generating system.
 28. The isolated phycobilisome of claim 22,wherein the phycobilisome comprises at least one protein encoded by eachof at least two different algal strains.
 29. The isolated phycobilisomeof claim 22, wherein the phycobilisome is reconstituted from a mixturecomprising an isolated phycobiliprotein or an isolated linker protein.30. The isolated phycobilisome of claim 22, wherein the phycobilisome isimmobilized on a manufactured solid support.
 31. An isolated,functionally intact phycobilisome comprising a plurality ofphycobiliproteins specifically connected by at least one linkerpolypeptide, wherein said phycobilisome is immobilized on a manufacturedsolid support.
 32. The immobilized phycobilisome of claim 31, whereinthe phycobilisome is stabilized.
 33. The immobilized phycobilisome ofclaim 31, wherein the phycobilisome is covalently attached to amolecular species selected from the group consisting of ligands,receptors, and signal-generating molecules.
 34. The immobilizedphycobilisome of claim 33, wherein said molecular species is attached toone type of constituent phycobilisome protein.
 35. The immobilizedphycobilisome of claim 33, wherein the molecular species is attached toa particular portion of the phycobilisome.
 36. The immobilizedphycobilisome of claim 31, wherein said phycobilisome comprises at leastone protein encoded by each of at least two different algal strains. 37.The immobilized phycobilisome of claim 31, wherein said phycobilisome isreconstituted from a mixture comprising an isolated phycobiliprotein oran isolated linker polypeptide.
 38. The immobilized phycobilisome ofclaim 31, wherein the phycobilisome is functionally coupled to asignal-generating system.
 39. The immobilized phycobilisome of claim 31,wherein the phycobilisome is a functional component of a biotransducer.40. The immobilized phycobilisome of claim 31, wherein the solid supportis selected from the group consisting of a synthetic membrane, apolymer, a microparticle, silicon, and glass.
 41. A manufactured solidsupport containing a plurality of immobilized phycobilisomes accordingto claim 31, said phycobilisomes being immobilized on the solid supportin a structurally ordered arrangement thereby forming a pattern on thesolid support.
 42. A manufactured solid support containing a pluralityof immobilized phycobilisomes according to claim 31, each phycobilisomebeing immobilized on the solid support in the same orientation withrespect to the solid support.
 43. An input system for a transducercomprising: conversion means for receiving ultraviolet or visible lightand directionally transferring light energy of said light; and couplingmeans for receiving said directionally transferred light energy anddelivering said light energy to a transducer.
 44. The system of claim43, wherein said coupling means comprises an optical fiber.
 45. Thesystem of claim 43, wherein said coupling means comprises a waveguide.46. The system of claim 43, wherein said conversion means comprises aphycobilisome.
 47. An environmentally responsive optical sensor,comprising: conversion means for receiving ultraviolet or visible lightand directionally transferring light energy of said light, whereintransfer of the light energy is dependent on an environmental condition;and sensor means for receiving said directionally transferred lightenergy and producing an indication of the environmental condition. 48.The environmentally responsive optical sensor of claim 47, wherein saiddirectionally transferred light energy comprises a photon of aparticular energy level, said energy level being dependent upon saidenvironmental condition.
 49. The environmentally responsive opticalsensor of claim 47, wherein said conversion means comprises aphycobilisome.
 50. A system for processing a light signal comprising:conversion means for receiving ultraviolet or visible light anddirectionally transferring light energy of said light; and processingmeans for receiving and processing said directionally transferred lightenergy.
 51. The system of claim 50, wherein said processing meanscomprises an optical fiber operative to transmit said light signal. 52.The system of claim 50, wherein said processing means comprises aphotosensor.
 53. The system of claim 50, wherein said directionallytransferred light energy comprises a photon.
 54. The system of claim 50,wherein said conversion means comprises a phycobilisome.
 55. A methodfor performing a specific binding assay comprising: contacting a samplecomprising an analyte with a specific binding partner; determining theamount of the analyte present in the sample by means of its ability tospecifically bind to the specific binding partner, wherein a componentof the assay is detectably labeled with a signal-generating systemcomprising phycobilisomes, said phycobilisomes being self-assemblingcomplexes of phycobiliproteins and linker proteins, each phycobilisomecomprising at least one rod, said assay component being selected fromthe group consisting of the specific binding partner, reagent moleculeshaving the same chemical identity as the analyte, and reagent moleculeswhich compete with the analyte for specific binding to the specificbinding partner.
 56. The method of claim 55, wherein an assay componentselected from the group consisting of a specific binding partner, areagent molecule having the same chemical identity as the analyte, and areagent molecule which competes with the analyte for specific binding tothe specific binding partner is attached to a solid phase.
 57. Themethod of claim 56, wherein the solid phase is selected from the groupconsisting of a synthetic membrane, a polymer, a microparticle, silicon,and glass.
 58. The method of claim 55, wherein the analyte is selectedfrom the group consisting of a nucleic acid, a drug, a ligand, anantigen, a hapten, an antibody, and a carbohydrate.